Protein Design & Biomolecular Models

Protein Design & Biomolecular Models. Recent publications parsed from OpenAlex.

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  1. bioRxiv (Cold Spring Harbor Laboratory)

    Discovering and designing multistate protein assemblies

    Chelsea N. Fries, Samuel W. K. Tipps, Adam J. Wargacki, Judith Ahr, Rebecca Skotheim, Connor Weidle, Justin A. Decarreau, Yang Hsia, Andrew J. Borst, Neil P. King

  2. bioRxiv (Cold Spring Harbor Laboratory)

    De novo design of light-controlled conformational protein switches

    Alexander T. Hilditch, Nicolas Manuel Goldbach, Chenxuan Liu, Luciano A. Abriata, Ann-Sophie Helene Kroell, Friederike C Reinhardt, Sabine Aschenbrenner, Natalia Gasilova, Sarah Carina Warrelmann, René Rasche, Yassine Faik, Kimali Pilet, Elisabetta Occelli, Sandrine Georgeon, Joseph H. Schmidt, Laure Menin, J. Standfuss, Josef Wachtveitl, Dominik Niopek, Bruno E. Correia

    Discovered via OpenAlex

  3. bioRxiv (Cold Spring Harbor Laboratory)

    Iterative Refinement for Structural Optimization of De Novo Protein Sequences

    Chance M Gammill, Lakshman S. Tamil

    Discovered via OpenAlex

  4. bioRxiv (Cold Spring Harbor Laboratory)

    Simulating protein evolution with programmable fitness objectives derived from modern protein models

    Kaiyu Qiu, Andrei N. Lupas, Stanisław Dunin-Horkawicz

    Discovered via OpenAlex

  5. bioRxiv (Cold Spring Harbor Laboratory)

    An Interactive Bidirectional De Novo Protein Design System

    Chance M Gammill, Lakshman S. Tamil

    Discovered via OpenAlex

  6. bioRxiv (Cold Spring Harbor Laboratory)

    Spatially enforced engagement of PD-1⁺ T cells with AXL⁺ cells reprograms the tumor microenvironment and overcomes anti-PD-1 resistance

    Ksenia M. Yegodayev, Gregory Perelman, Tamar Shami, Bar Kaufman, Danialle Raviv, Divyasree Marripati, Aseel Khateeb, Raz Ben-Uri, Oshrat Galibov-Levi, Idan Milo, Alice Raizman, Alona Veinblat, Abraham Nissani, Noam Zuri, Dinesh Babu Manikandan, Ekaterina Rudnitsky, Ofra Novoplansky, Jonatan Zorea, Sarah Adi Eisdorfer, Sankar Jagadeeshan, Gili Ezri, Kamran Waidha, Raghda Abu Shareb, Monica Wainer, Uzi Hadad, Orit Itzhaki, Ronnie Shapira‐Frommer, Yochai Wolf, Merav Cohen, Kong De, Hai Wang, Angel Porgador, Leeat Keren, Amir Aharoni, Yaron Carmi, Ofir Cohen, Moshe Elkabets

    Discovered via OpenAlex

  7. bioRxiv (Cold Spring Harbor Laboratory)

    Function-preserving CD8⁺ T Cell Immunogenicity minimization through protein design

    Bingxu Liu, Tianyang Mao, Max H. Witwer, Oliver Morell, Nir Hacohen, David A. Baker

  8. Journal of Chemical Information and Modeling

    Design Trade-Offs between Target Binding and Self-Association Revealed by De Novo SARS-CoV-2 Binders

    Lourdes Carcelén, Daniel Peñas-Utrilla, Diego S. Ferrero, Cristina Ferrer‐Orta, Marta Nadal, Francesco Colizzi, Juana C. Muñoz, Marta Taulés, Núria Verdaguer, Enrique Marcos

    Discovered via OpenAlex

  9. Theoretical and Natural Science

    Advances in Application of ESM3 and Multimodal Generative Protein Language Models in Intelligent Design of Antimicrobial Peptides

    Shang Wang

    Discovered via OpenAlex

  10. bioRxiv (Cold Spring Harbor Laboratory)

    Computational Design and Evaluation of De Novo Protein Minibinders Targeting Specific Sites of STAT3

    Emily R Sragovicz, Alexander V. Tobias

    Discovered via OpenAlex

  11. Antibody Therapeutics

    Integrated AI-Guided de novo CDR-H3 Design and Combinatorial Phage Display for Antibody Discovery

    Kairi Furui, Shinji Soga, Rika Yamazaki, Shigenori Yagi, K. Uchikawa, Takatsugu Kosugi, Takuya Shimomura, Kana Gondo, Masahito Ohue

    Discovered via OpenAlex

  12. bioRxiv (Cold Spring Harbor Laboratory)

    Design of full-length agonist and antagonist antibodies for hard targets

    Pythia Labs Team, Robin A. Aglietti, Ramin Ansari, Peter M. Bowers, Tim-Henrik Buelles, Hadrien Chauvin, Thibault M. Duplay, Mohamed El Hibouri, Julien Jorda, Joshua Laniado, Matthias M. A. Malago, Kyle Meador, Anya Polovina, Katty Polyak, Justyna Sosna, Robert Tacke, Todd O. Yeates, Lucas Zanini

    Discovered via OpenAlex

  13. bioRxiv

    Can Folding Models Tell Binders from Bluffers? Evidence from POISK: The Patent-Derived Antibody Dataset

    Tupikina, D, Roncoli, A, Bujotzek, A, Abanades, B

    Discovered via OpenAlex

    Preprint source: bioRxiv: Bioinformatics

  14. Nature Communications

    Designing rigid protein fiducials to visualize GPCR conformational states

    Alina Vo Vo, Yuan-En Sun, Justin G. English, Michael J. Robertson

    Discovered via OpenAlex

  15. Nature Communications

    Predicting protein electrostatics with protein language models

    Mingzhe Shen, Guy W. Dayhoff, Daniel Kortzak, Jana Shen

    Discovered via OpenAlex

  16. bioRxiv

    Projected Gradient Descent for Hallucination-Based Protein Binder Design

    Ross, M, Miller, D, Wells, J

    Discovered via OpenAlex

    Preprint source: bioRxiv: Bioinformatics

  17. bioRxiv

    UnibindMD: An Integrated AI and Molecular Dynamics Platform for De Novo Peptide Binder Design

    Wu, X, Huang, A, Fu, C, Wang, Z, Fu, W

    Discovered via OpenAlex

    Preprint source: bioRxiv: Bioinformatics

  18. Annual Review of Microbiology

    Computational Peptide Design: Emerging Concepts in Antibiotics, Immunity, and Evolution

    Sihan Chen, Xiaoyu Wang, Fuyi Li, Octávio Luiz Franco, Jiangning Song, César de la Fuente‐Núñez

    Discovered via OpenAlex

  19. Journal of Chemical Information and Modeling

    HEIWA: Hybrid Explicit–Implicit Water Attention Affects Force Field Accuracy in Structure-Based Protein Language Model ESM3

    Ngai Hei Ernest Ho, Chao‐Tung Yang, I‐Son Ng, Jo‐Shu Chang

    Discovered via OpenAlex

  20. arXiv (Cornell University)

    Computational De Novo Design of Miniprotein Candidate Neutralizers Targeting the IL-23 Cytokine Subunit p19

    Raghav Paladugu, Fardina Fathmiul Alam

    Discovered via OpenAlex

  21. Frontiers in Bioengineering and Biotechnology

    Design and validation of nucleosome binding peptides using BindCraft

    Pavel D. Oleinikov, Grigoriy A. Armeev, Alina E. Sidorkina, Elizaveta B. Rykunova, Galina A. Komarova, Nikita A. Motorin, Nadezhda S. Gerasimova, Alexey V. Feofanov, Vasily M. Studitsky, Alexey К. Shaytan

    Discovered via OpenAlex

  22. Microorganisms

    From Waste to Wealth: Integrating Biological Systems and Molecular Intelligence for Lignin Valorization

    Hailin Zhang, Renqiang Li, Suyao Yin, Xu Zhang, Carol Sze Ki Lin, Cuijuan Gao, Jingjing Liu

    Discovered via OpenAlex

  23. Advanced Functional Materials

    Neuron Mitochondria Targeted “Zipper Peptide” Delivery for VHL‐Inhibiting Therapy in Parkinson's Disease

    Yiming Cao, Hao Cheng, Haohui Ding, Xiaochen Liu, Junqiu Ye, Jiawei He, Yueqian Zhou, Mengyu Gu, Guochen Han, Xiangdong Gao, Yang Ding, Song Chen

    Discovered via OpenAlex

  24. bioRxiv

    Active Learning framework for Antibody Binding Affinity Prediction

    Krishna, C. S, Singh, H, Srivastava, S. P, SINGH, R. K

    Discovered via OpenAlex

    Preprint source: bioRxiv: Bioinformatics

  25. Analytical Chemistry

    De Novo Design Peptide Probe Enables Super-Resolution Imaging of MFGE8−Integrin Nanoscale Signaling Platforms in Triple-Negative Breast Cancer

    Sennan Qiao, Jing Gao, Hongda Wang, Chuang Ma, Haijiao Xu, Zhenyan Jiang, Liqun Ren

    Discovered via OpenAlex

  26. ChemRxiv

    VHH-Bench: A Benchmarking Framework for Evaluating Nanobody–Antigen Complex Predictions Across CDR3 Conformations

    Nehad S. El Salamouni, Qiang Zhu, Haibo B. Yu

    Discovered via OpenAlex

  27. bioRxiv (Cold Spring Harbor Laboratory)

    Design of readers for pathological PTM proteoforms in Alzheimer’s disease

    Kejia Wu, Tiana Schantz, Lemuel Chang, Prarthna Chabria, Elaina Bashaw, Thejesh Reddy Kalatturu, Doo Yeon Kim, An‐Qi Chen, Nathaniel Corley, Asim K. Bera, Alex Kang, Hannah Nguyen, Johnny Mendoza, Xinting Li, Magnus S. Bauer, Misa Baum, Brian C. Kraemer, Yuyu Song, David A. Baker

  28. Nature

    De novo design of enantioselective artificial metalloenzyme photocatalysts

    Sandip Mishra, Payal, Declan Evans, Kingsley Bortey, Husayn Bootwala, Giovanni González-Gutiérrez, Ricardo Javier Vázquez, David Baker, Jared C. Lewis

  29. Nature

    Programmable design of functional proteins from natural language

    Fengyuan Dai, Shiyang You, Yudian Zhu, Yuan Gao, Lihao Fu, Xibin Zhou, Jin Su, Chentong Wang, Yuliang Fan, Qingsong Tan, Xiaoxiao Ma, Xianjun Deng, Letong Yu, Hui Qian, Yan He, Yitao Ke, Zhe Zhang, Chenchen Han, Xing Chang, Liangzhen Zheng, Sheng Wang, Yuan Ji, Kexin Hao, Longxing Cao, Yajie Wang, An‐Ping Zeng, Shunzhi Wang, Chunjun Zhan, Jing Zhao, Tong Si, Jianming Liu, Hongyuan Lu, Fajie Yuan

    Discovered via OpenAlex

  30. Biomolecules

    Structure–Function Relationships of Cid1 Poly(U) Polymerase: Catalysis, Substrate Recognition, Engineering, and Applications

    Yang Chen, Pengbo Wang, Mingdong Yao, Quanyong Liu, Kian Mau Goh, Shoutao Zhang

    Discovered via OpenAlex

  31. Sensors and Actuators B Chemical

    Fragment assembly-driven De novo engineering of cyclic peptide scaffolds for fluorescent biosensing: A novel strategy for small-molecule detection

    Zhenqi Sun, Sibo Shi, Lihong Yu, Jun Liu, 庞月红, Xiaofang Shen

    Discovered via OpenAlex

  32. An AI-Driven Peptide Optimization Chatbot for Therapeutic Design: Integrating Machine Learning Models with Pharmaceutical Formulation Intelligence

    Ph.D. Michael Sekar, MS Deepakraja Rajendran, Anand Paul Sekar

    Discovered via OpenAlex

  33. bioRxiv (Cold Spring Harbor Laboratory)

    Sequence-only prediction of VHH nanobody epitopes and paratopes on HER2 with a frozen protein language model ( ESM2) and a structure-derived residue prior

    Dharani Babu, Sundaramurthy Pandurangan

    Discovered via OpenAlex

    Preprint source: bioRxiv: Bioinformatics

  34. bioRxiv (Cold Spring Harbor Laboratory)

    Reliable and Efficient Agentic Protein Design with Toolset Harnessing

    Jasper Butcher, Jie Chen, Andrew Hunt, Cyrus M. Haas, Wenzhao Dai, Shajesh Sharma, Raktim Mitra, Saman Salike, Jeremy G. Koob, Aiko Muraishi, Zhe Li, Harley Pyles, Michael Dominik Tyka, Magnus S. Bauer, Rafi I. Brent, Anant Mittal, Neil P. King, David Baker

  35. Organic Communications

    Computational investigation of myoferlin-C2D-targeting potent peptides

    Özgür Yılmaz, Fulya Çağlar

    Discovered via OpenAlex

  36. bioRxiv (Cold Spring Harbor Laboratory)

    Bypassing Current Biosecurity Screens with AI Designed Proteins and Closing the Gap with Edge-AI Functional Screening

    Mackenzie Noon, Grace Oualline

    Discovered via OpenAlex

    Preprint source: bioRxiv: Bioinformatics

  37. bioRxiv (Cold Spring Harbor Laboratory)

    Holistic Design of Selective Photoenzymes with Genetically Programmed Sensitizers

    Florence J. Hardy, Rebecca Crawshaw, Christophe Didier, Anna Kohn, Francis J. Gallois, Anna Lauko, Samuel J. Pellock, Indrek Kalvet, Anthony P. Green, David A. Baker

  38. Zenodo (CERN European Organization for Nuclear Research)

    CHIEF: An Attention-based Ensemble Learning Framework for Functional Protein Inverse Folding

    Geng Zilong

    Discovered via OpenAlex

  39. Nature Communications

    Rapid assessment of chemical complementarity of ligands for protein design

    Rokas Petrenas, Katarzyna Ożga, Joel J. Chubb, Andrey V. Romanyuk, Dominic Alibhai, Jennifer J. McManus, Graham J. Leggett, Nigel Shaun Scrutton, Thomas A. A. Oliver, Derek N. Woolfson

    Discovered via OpenAlex

  40. ChemRxiv

    DeImmu-MPNN: Reducing Immunogenicity in De Novo Protein Design

    Niklas Halbwedl, Sebastian Springer, Martin Zacharias

    Discovered via OpenAlex

  41. Journal of the American Chemical Society

    Native Mass Spectrometry-Based Proteoform Explicit Metrics System (PrEMS) Informs Structural Improvement of Artificial Photocyclase Enzymes

    Mengmeng Zhang, Long Shi, Yaming Deng, Z.‐D. LIU, Haoyun Lu, X Wang, Yayu Qiu, Fangrui Zhong, Zhaoming Liu, Qi Wang, Ruikang Tang, Y H Wu, Mowei Zhou

    Discovered via OpenAlex

  42. Nature Chemical Engineering

    Agents intuit enzyme design

    Thomas Dursch

    Discovered via OpenAlex

  43. bioRxiv (Cold Spring Harbor Laboratory)

    CAPO: Compute-Aware Automated Protein-Model Optimization

    Theo Schifferli, J. García Pardiñas, Edward B. Irvine, Mary‐Anne Hartley, Thomas Bikias

    Discovered via OpenAlex

    Preprint source: bioRxiv: Bioinformatics

  44. arXiv (Cornell University)

    Aptamers as a sandbox for lab-in-the-loop agentic molecular discovery

    Zachary Cutts, John Coller, Rachel Chen, Hua Tang, Mathias Bellaiche, Ryder Easterlin, Dina Zverinski, Petar Sirkovic, Avinatan Hassidim, Yossi Matias, Pooja Rao, Annalisa Pawlosky

    Discovered via OpenAlex

  45. npj Science of Food

    De novo design of protein binders targeting the human sweet taste receptor as potential sweet proteins

    Saisai Ding, Yi Zhang

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.3 RoseTTAFold-based

  46. bioRxiv (Cold Spring Harbor Laboratory)

    MYC targeted de novo binders impair tumor growth

    Nora K. McNamara-Bordewick, Kejia Wu, Yulong Su, Assmaa ElSheikh, Xiaoyan Wang, Melissa Cunningham, Colin Daniel, Rosalie C. Sears, Robert N. Eisenman, David A. Baker

  47. Scientific Reports

    Representation learning for low-data protein fitness prediction using sequence–structure embeddings and graph neural networks

    Chanoknun Phunnasorn, Narupat Hongdilokkul, Wasakorn Laesanklang, Charin Modchang, Tipaluck Krityakierne

    Discovered via OpenAlex

  48. Frontiers in Immunology

    Real-time exploration of the billion-scale human repertoire for precursor frequency analysis and rational antibody design

    Tom U. Schlegel, Jannis von Blanckenburg de Riz, Jakob R. Riccabona, Franz Dietzmeyer, Julia Koehler Leman, Jens Meiler, Clara T. Schoeder, Torben Schiffner

    Discovered via OpenAlex

  49. European Journal of Medicinal Chemistry

    HighPlay3: Structure-Integrated de novo cyclic peptide design balancing binding affinity and membrane permeability

    Renjie Zhu, Chengyun Zhang, Hu Haomeng, Yutong Ge, Yan Xie, CHONGYANG LI, Wentong Wang, Jingjing Guo, Xudong Wang, Hongliang Duan

    Discovered via OpenAlex

  50. bioRxiv (Cold Spring Harbor Laboratory)

    De novo design of metalloenzymes using Metal Mer

    Chuan Shan, Zhuoyun Ren, Jiong Yu, Yuan Gao, Chenxin Wu, Xiaofang Zhong, Lei Lu

    Discovered via OpenAlex

  51. Research Square

    EZPro-Fit: A Thermophile-Informed Cross-Modal Generative Framework Integrating DNA Language and Protein Structure for Enzyme Mutant Design

    Ran Xu, Zhao Linyan, Ronghua Pei, Yan Xu, Zhiyuan Zhou, Hongliang Duan, Leyi Wei, Liangzhen Zheng, Dongyang Liu, Jingjing Guo

    Discovered via OpenAlex

  52. arXiv (Cornell University)

    Revisiting Structure-Based Filtering for AI-Designed Antibodies: Opportunities, Limits, and What Matters

    Langzhang Liang, Junchen Qian, Xiaojie Ma, Mingxi Zou, Yinghui Xu, Zenglin Xu, Tianlei Ying

    Discovered via OpenAlex

  53. Zenodo (CERN European Organization for Nuclear Research)

    Feature Engineering for Biological Sequence and Protein Structure Prediction

    Filip Markovic

    Discovered via OpenAlex

  54. Science

    Atomic functional site scaffolding in biopolymers with RFdiffusion3

    Jasper Butcher, Rohith Krishna, Raktim Mitra, Seth M. Woodbury, Donghyo Kim, Rafael I. Brent, Yanjing Li, Nathaniel Corley, Andrew Favor, An‐Qi Chen, Paul T. Kim, Jonathan Funk, Gabriela Bastidas Reinoso, Kejia Wu, Aiko Muraishi, Helen E. Eisenach, Saman Salike, Simon V. Mathis, Tuscan Rock Thompson, Antonia Ruder, Enisha Sehgal, Andrew Kubaney, Jie Chen, Yuliya Politanska, Brian Coventry, Odin Zhang, Florence J. Hardy, Bo Qiang, Kieran Didi, Maxwell W. Kazman, Lars L. Schaaf, Frank DiMaio, David A. Baker

  55. ChemRxiv

    De novo design of photoenzymes with substrate-recognition-encoded enantioselectivity

    Zehui Wang, Yangjinxiu Zhou, Yunhao Li, Guojiao Wu, Mengwen Shi, Siyuan Wang, Tengfei Pang, Yuqi Peng, 俊弟 郭, Huiyi Zhou, Yingru Xu, Hongmei Liu, Mowei Zhou, Xi Chen, Pengfei Ji, Fangrui Zhong, Yuzhou Wu

    Discovered via OpenAlex

  56. arXiv (Cornell University)

    Poisoning the corpora of protein design systems during pre-training and retrieval

    Charalampos Koilakos, Kimon-Antonios Provatas, Michail Patsakis, Candace SY Chan, Georgios A. Pavlopoulos, Ilias Georgakopoulos‐Soares

    Discovered via OpenAlex

  57. Peptide agonist design from GPCR sequences

    Binbin Xia, Xingzheng Wang, Qiuxiang Tan, 西干, Yixin Niu, Junhao Zhu, Yanjie Li, Rui Ma, Qiang Zhao, Longchao Liu, Jun Wang

    Discovered via OpenAlex

  58. Scientific Reports

    Integrated sensor engineering and AI-assisted peptide design to target the Zika virus NS2B-NS3 protease

    Alejandro Cadillo-Valverde, Ana Sanchez-Castro, Pohl Milón

    Discovered via OpenAlex

  59. Nature

    Computational design of metalloproteases

    An‐Qi Chen, Kejia Wu, Hojae Choi, Preetham Venkatesh, Samuel J. Pellock, Nikita Hanikel, Hojeong Shin, Declan Evans, Kieran Didi, Lars L Schaaf, Cristina Díaz‐Perlas, Brian Coventry, Donghyo Kim, Seth M. Woodbury, Pengfei Ji, Shingo Honda, Asim K. Bera, Hannah Nguyen, Alex Kang, Yanqing Wang, Xinting Li, Stacey Gerben, Lemuel Chang, Xiao Yan, Benjamí Oller‐Salvia, Anthony A. Hyman, Donald Hilvert, David A. Baker

    Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.3 RoseTTAFold-based

  60. Nature

    De novo design of cysteine proteases

    Hojae Choi, Magnus S. Bauer, Brian Coventry, Preetham Venkatesh, An‐Qi Chen, Donghyo Kim, Asim K. Bera, Alex Kang, Hannah Nguyen, Shayan Sadre, Justin A. Decarreau, Emily Joyce, Bhanumathi Shankaran, Tuscan Rock Thompson, Gabriel Greenstein, Kieran Didi, Lars L Schaaf, Jacob Merle Gershon, Alexander F. Shida, Gyu Rie Lee, Donald Hilvert, Samuel J. Pellock, David A. Baker

    Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.3 RoseTTAFold-based

  61. Journal of Medicinal Chemistry

    Medicinal Chemistry Strategies for Targeting RNA-Binding Proteins: Design, Optimization, and Therapeutic Potential

    Bangbang Li, Hao Shen, Zeliang Xu, Yixi Wang, Jiayu Ding, Zhongrui Shi, Chengliang Sun, Peng Yang, Xiao Wang

    Discovered via OpenAlex

  62. bioRxiv (Cold Spring Harbor Laboratory)

    Programming Targeted Immune Cell Migration Using Orthogonal Chemokine-Receptor Pairs

    Jungmin Lee, Karthik Srinivasan, Claudia Llinás del Torrent, Debraj Ghose, Devan H Shah, Luis Oliva Hernandez, Sarah Wasinger, Michelle Chang, Wei Yu, Yurie Tonai, Francis C. Peterson, Martyna Szpakowska, Andy Chevigné, Brian F. Volkman, Aashish Manglik, Wendell A. Lim

    Discovered via OpenAlex

  63. arXiv (Cornell University)

    InstructPro2: Natural Language and Biological Grounding Guided De Novo Protein Design

    Charles Novak, Zhenqiao Song, Chuan Li, Jianwen Xie, Lei Li

    Discovered via OpenAlex

  64. arXiv (Cornell University)

    ReproBAIT: Can coding agents build their own biological AI tools?

    Shiv Muthupandiyan, Tolga Hasan Dur, Mac Walker, Timo Flesch, Mahmoud Ghanem, Steph Suddell, Giles Harper-Donnelly, Sophie Rose, Jasper Götting, Coleman Breen, Jake Pencharz

    Discovered via OpenAlex

  65. ChemRxiv

    De Novo Design of Enantioselective Artificial Metalloenzyme Photocatalysts Containing Metal Polypyridine Cofactors

    Sandip Mishra, Payal, Declan Evans, Kingsley Bortey, Husayn Bootwala, Giovanni González-Gutiérrez, Ricardo Javier Vázquez, David A. Baker, Jared C. Lewis

  66. bioRxiv (Cold Spring Harbor Laboratory)

    Computational design of protein conformational landscapes for metamorphic behavior

    Alisa Khramushin, Maddalena Elia, Christian Schellhaas, Alberto Borsatto, Joseph H. Schmidt, Mohamad Yazan Chabaan, Roberta Pierattelli, Kelvin Lau, Francesco Luigi Gervasio, Luciano A. Abriata, Bruno E. Correia

    Discovered via OpenAlex

  67. arXiv (Cornell University)

    Multi-Objective Amortized CDRH3 Sequence Sampling Diversifies Promising Antibody Candidates

    Joseph D. Viviano, Almer M. van der Sloot, Quentin Fournier, Robert McCoy Vernon, CHRISTOPHER JAMES LANGMEAD, Yoshua Bengio

    Discovered via OpenAlex

  68. ChemRxiv

    CP-GFM-SGX: Topology-Aware Cyclic Peptide Generation and Design with Receptor-Conditioned Structural Evaluation and Experimental KRAS Affinity Optimization

    Zhiyuan Hu, Russell Dillworth

    Discovered via OpenAlex

  69. bioRxiv (Cold Spring Harbor Laboratory)

    Chain of Structures: Connecting Reasoning and Generation for Protein Design

    Qingran Cai, Mingyang Xu, Jiaxian Yan, Zhicai Wang, Yufeng Liu, Qizhi Pei, Zaixi Zhang

    Discovered via OpenAlex

    Preprint source: bioRxiv: Bioinformatics

  70. ACS Omega

    Simulating Directed Evolution In Silico with an Iterative, Physics-Based Workflow

    Chey M. Jones, Deeptak Verma

    Discovered via OpenAlex

  71. bioRxiv (Cold Spring Harbor Laboratory)

    Filling the Missing Puzzle: Integrating Interaction and Evolutionary Information to Enhance Protein Fitness Prediction in Inverse Folding

    Zhihao Wang, Zhongyang Zhang, Yanmei Yang, Yuanyuan Qu, Yuguang Mu, Sheng Wang, 韩楠玉, Liangzhen Zheng, Weifeng Li

    Discovered via OpenAlex

  72. bioRxiv (Cold Spring Harbor Laboratory)

    PeTFlow: Flow-Matching Based All-Atom Peptide Design through Side-Chain State Tokenization

    Qirui Deng, Mingyuan Xu, Chen Hong-ming, Jinping Lei

    Discovered via OpenAlex

  73. arXiv (Cornell University)

    DC-Flow: Target-Conditioned Cyclic Peptide Design via Delayed-Coupling Flow Matching

    Yitian Wang, Minjie Cheng, Yaning Cui, Maohua Yang, Dongdong Wang, Hongteng Xu

    Discovered via OpenAlex

  74. Biomolecules

    Artificial Intelligence-Driven Nanobody Engineering for Pathogen Recognition: From Functional Epitope Prioritization to Multimodal Foundation Models

    Rui-Si Hu, Muhammad Ehsan, Wei Luo, Jian Zhou, Yongle Xiao, He-Xin Wang, Cheng-Yang Li, Kui Gu

    Discovered via OpenAlex

  75. bioRxiv (Cold Spring Harbor Laboratory)

    De Novo Design of Flavoproteins with Controlled Excited State Dynamics

    Ethan L. Bungay, Juno Underhill, Liu Meiyue, Alexandra N. Stuart, Catherine R. Back, Jessica C. Berrones‐Reyes, Paulina Dubiel, James A. Birrell, Aditya G. Rao, Christopher Williams, Rob Barringer, Philip Hinchliffe, Bruce R. Lichtenstein, Basile F. E. Curchod, Julea N. Butt, Thomas A. A. Oliver, Adrian John Mulholland, J. L. Ross Anderson

    Discovered via OpenAlex

  76. bioRxiv (Cold Spring Harbor Laboratory)

    Buried Ion-Pairs Reshape Folding Pathways of Artificial Proteins

    Jobst Liebau, Grant Kemp, Dirk Auman, Niklas Hoja, Alexander Jussupow, Mona Baumgart, Gunnar von HEIJNE, Ville R. I. Kaila

    Discovered via OpenAlex

  77. arXiv (Cornell University)

    Joint Discrete and SE(3) Diffusion for Protein Interface Design

    Zhenqiao Song, Jianwen Xie, Lei Li

    Discovered via OpenAlex

  78. Nature Communications

    De novo design of miniprotein inhibitors of bacterial adhesins

    Adam M. Chazin-Gray, Tuscan Rock Thompson, Edward D. B. Lopatto, Pearl Magala, Patrick W. Erickson, Andrew C. Hunt, Anna A. Manchenko, Pavel Aprikian, Veronika L Tchesnokova, Irina Basova, Denise A. Sanick, Kevin O. Tamadonfar, Morgan R. Timm, Jerome S. Pinkner, Karen Dodson, Alex Kang, Emily Joyce, Asim K. Bera, Aaron J. Schmitz, Ali H. Ellebedy, Kelli L. Hvorecny, Gianluca Interlandi, Mark J. Cartwright, Andyna Vernet, Sarai Bardales, Desmond White, Rachel E. Klevit, Evgeni V. Sokurenko, Scott J. Hultgren, David A. Baker

  79. bioRxiv (Cold Spring Harbor Laboratory)

    De novo protein design in an expanded chemical space

    Yuxuan Li, Yanbo Jing, Yeyu Su, Wei Ren, Jing Zhang, Tao Liu

    Discovered via OpenAlex

  80. arXiv (Cornell University)

    Designing Protein Structures from Natural Language

    Joseph Lee, Yanjing Li, Bo Qiang, Lau G, Allyson Ettinger, Noah A. Smith, Rory Donovan-Maiye, David Baker, Hanna Hajishirzi, Pang Wei Koh

  81. Journal of Chemical Information and Modeling

    Sequence Dependence of Folding and Self-Assembly of Glycine-X Repeat Peptides on Graphite

    Eduardo Cubillos-Llantén, Julius A. Neumann, Horacio Poblete, Jeffrey R. Comer

    Discovered via OpenAlex

  82. Current Bioinformatics

    AttentionRBP: Integrating Multimodal Features via Sparse Cross- Attention for RNA-Binding Protein Prediction

    Baolu Shi, Bowen Li, Zhi-Ping Liu

    Discovered via OpenAlex

  83. bioRxiv (Cold Spring Harbor Laboratory)

    Programming N-linked glycan composition through de novo protein design

    Margaret C. Lunn-Halbert, Joel D. Allen, Rohith Krishna, Манченко Анна, Xinting Li, Edward D. B. Lopatto, Jerome S. Pinkner, Carolina Möller, Woody Ahern, Johnny Mendoza, Alex Kang, Hannah Nguyen, Emily Joyce, Asim Bera, Scott J. Hultgren, Evgeni V. Sokurenko, Max Crispin, David A. Baker, Neil P. King

  84. Results in Engineering

    SMP103: a de novo-engineered macrocyclic peptide binder candidate targeting the virulence-associated transpeptidase Sortase A

    Olanrewaju Ayodeji Durojaye, Soukayna Baammi, Mohamed Moussaoui, Salaheddine EL HADAD, Loubna Alimoussa, Rachid Benhida, Rachid Daoud

    Discovered via OpenAlex

  85. bioRxiv (Cold Spring Harbor Laboratory)

    Generalizing Protein Fitness Prediction Across Distribution Shifts via Structural and Co-evolutionary Priors

    Nopsinth Vithayapalert, Maytus Piriyajitakonkij, Francesca Grisoni

    Discovered via OpenAlex

  86. arXiv (Cornell University)

    De novo design of monoclonal and bispecific antibodies with OFAntibody

    Valhalla Team

    Discovered via OpenAlex

  87. ACS Catalysis

    Machine Learning Empowers Enzyme Discovery, Structure Prediction, Engineering, and Design

    王木强, Ling Jiang, Haoran Yu, Jiachen Yu, Wenlong Zheng, Jianmin Wu

    Discovered via OpenAlex

  88. International Journal of Molecular Sciences

    Enhancing the Activity of Ribokinase from Thermus sp. 2.9 Through Rational Design for the Cascade Synthesis of Modified Nucleotides and Nucleosides

    Evgeniy A. Zayats, Yuliya A. Abramchik, Maria A. Kostromina, И. В. Фатеев, Andrey A. Karanov, Alexandra R. Sharafutdinova, Vasiliy A. Ptushkin, Ирина Дмитриевна Константинова, Andrey V. Golovin, Р. С. Есипов

    Discovered via OpenAlex

  89. bioRxiv (Cold Spring Harbor Laboratory)

    Complex enzyme active site scaffolding by iteratively detuned catalytic guidance

    Tingli Qian, Weijin Wang, Shilong Gao, Aiko Muraishi, Beibei Zhao, Davi Nakajima An, Fanglei Xue, Max Kazman, Johnny Mendoza, Hannah Nguyen, Asim Bera, Alex Kang, Avery Yang, Wenzhao Dai, Jia Liang, Yujia Wang, Xiongyi Huang, Frank DiMaio, David A. Baker

  90. bioRxiv (Cold Spring Harbor Laboratory)

    PepRePs: Peptide-Retargeted Phosphatases Designed with Generative Language Models

    Lauren Hong, Tai-Chen Ho, Yi-Shiuan Tseng, Sophia Vincoff, Tong Chen, Thomas Connor Donahue, Matthew P. DeLisa, Po‐Han Chen, Pranam Chatterjee

  91. Communications Materials

    A diversified approach to the design of recombinant silk proteins for biomaterials

    Alexandra E. Coram, Thomas A. Campbell, Colin J. Jackson, Adam Willis Perriman

    Discovered via OpenAlex

  92. Research Square

    Choosing protein design models with limited experimental measurements

    Michael Doane

    Discovered via OpenAlex

  93. bioRxiv (Cold Spring Harbor Laboratory)

    Joint protein, mRNA and DNA sequence design and optimization with nucleotide-level Potts models

    Błażej Banaszewski, L Dornfeld, Dexiong Chen, Karsten Michael Borgwardt, Lukas F. Milles

    Discovered via OpenAlex

  94. ACS Nutrition Science

    AI-Guided De Novo Design Pipeline for Oral, Gut-Active Peptides That Stimulate GLP-1 Secretion and Promote Weight Loss in Diet-Induced Obese Rats

    Eden Goldfarb, Lucia Adriana Lifshits, M.M. Abramov, Daniel Zvi Bar, Zohar Barbash, Eyal Akiva, Maayan Gal

    Discovered via OpenAlex

  95. Nucleic Acids Research

    CLEAN Database: providing enzyme function coverage for over 55 million sequences

    Le Yuan, Jianan Canal Li, Miaoyuan Wen, David M. Bianchi, Katherine Arneson, Bingji Guo, Sara Lambert, Chris Stephens, Tianhao Yu, Lijiang Fu, Christopher Pond, Matthew J. Berry, Huimin Zhao

    Discovered via OpenAlex

  96. Journal of Biomolecular Structure and Dynamics

    Integrating deep learning model for precision design of MERS antibodies with augmented affinity against SARS-CoV-2

    Areesha Irshad, Atta Ur-Rehman, Taskeen Koser, Mudasir Alvi, Hunza Usman, Rana Rehan Khalid

    Discovered via OpenAlex

  97. Bioinformatics Advances

    PRIZM: Combining Low-N Data and Zero-shot Models to Design Enhanced Protein Variants

    David Harding-Larsen, Brianna M. Lax, Martina Escorial García, Catarina Mendonça, Felipe Mejia-Otalvaro, Ditte Hededam Welner, Stanislav Mazurenko

    Discovered via OpenAlex

  98. Frontiers in Bioengineering and Biotechnology

    Advances and applications of engineered protein therapeutics and their role in precision medicine

    Wadha Aldossary, Nada Alqahtani, Layla Asiri, Noora Alkhurayef, Samar Alagl, Sana Alturki, Duha Saad, Mashael Al Yahya, Samah Al-Harthi

    Discovered via OpenAlex

  99. arXiv (Cornell University)

    Valid Stopping in Adaptive Generator-Verifier Loops

    Mahmoud Hegazy, Michael I. Jordan, Aymeric Dieuleveut

    Discovered via OpenAlex

  100. ACS Catalysis

    Molecular Dynamics Simulations Empowered De Novo Design of Binding Peptide for Enhanced Direct Bioelectrocatalytic Oxygen Reduction

    Xiufeng Wang, Meng Zhang, Hejian Zhang, Weisong Liu, Shuaiqi Meng, Lingling Zhang, Haiyang Cui

    Discovered via OpenAlex

  101. bioRxiv (Cold Spring Harbor Laboratory)

    Designing enzymes for new-to-nature chemistry and non-natural substrates with AlphaProtein Novo

    Zachary Wu, Josh Abramson, Thomas Frerix, Alexander E. Chu, Ruijie K. Zhang, Luca Schulz, Amy E. Danson, Tristan O. C. Kwan, Li Kevin Wenliang, Jacob Kelly, Zi‐Qi Li, Rosalia G. Schneider, Ashok Thillaisundaram, Harshnira Hitesh Patani, Vinícius Zambaldi, Sukhdeep Singh, David La, Masy Domecillo, Ariane Mora, Julia C. Reisenbauer, Yu Zhang, Eliseo Papa, Akvilė Žemgulytė, Yuhan Wu, Augustin Žídek, Jiaxin Shi, Grace Margand, Naila Assem, Kate Stephen, Charles A. Emrich, Peng Liu, Lucy J. Colwell, Demis Hassabis, Rob Fergus, Frances H. Arnold, Pushmeet Kohli, Jue Wang

    Discovered via OpenAlex

  102. arXiv (Cornell University)

    Bridging the Evidence-to-Execution Gap:A Reflective Agent for Multi-Objective Peptide Design

    Haosen Zhang, Yang Yang

    Discovered via OpenAlex

  103. Biophysical Reviews

    Protein engineering in Brazil: a biophysical perspective

    Mariana Zuliani Theodoro de Lima, Gustavo Foltran Umbehaun, Atílio Tomazini

    Discovered via OpenAlex

  104. Frontiers in Chemistry

    Engineering a hemoglobin variant with enhanced stability and oxygen affinity using a protein language model

    Sergey Shityakov, Alexander S. Novikov, Екатерина Владимировна Скорб, Thomas Dandekar

    Discovered via OpenAlex

  105. Chem & Bio Engineering

    Rate-Limiting Enzyme Design in Propionaldehyde Oxidation-Driven Dual-Cofactor Regeneration System

    Zebin Liu, Hui Ren, Yaoyao Zhao, Hanchi Chen, Jianguo Wang

    Discovered via OpenAlex

  106. bioRxiv (Cold Spring Harbor Laboratory)

    Design-Evolution Synergy Enables New-to-Nature Enzyme Chemistry

    Zi‐Qi Li, Ruijie K. Zhang, Pei‐Pei Xie, Jacob Kelly, Yu Zhang, Ziyang Qin, Théophile Lambert, Orna Mukhopadhyay, Deirdre Hanley, Amy E. Danson, Josh Abramson, Sukhdeep Singh, Zachary Wu, Pushmeet Kohli, Peng Liu, Jue Wang, Frances H. Arnold

    Discovered via OpenAlex

  107. arXiv (Cornell University)

    Evaluator-in-the-Loop Monte Carlo Tree Search via LLM Agents for Motif Scaffolding in Protein Design

    Haotian Hu, Oguzhan Gungordo, Siheng Xiong, Faramarz Fekri

    Discovered via OpenAlex

  108. Frontiers in Bioengineering and Biotechnology

    Collagen targeted self-anchoring antimicrobial molecular agents

    Nur Ceren Selcuk, Erhan Demirel, Stephen C. Waller, Malcolm L. Snead, Paulette Spencer, Candan Tamerler

    Discovered via OpenAlex

  109. Nucleic Acids Research

    DRAMP 5.0: an update integrating sequence and structure in a novel FASTS format for AI-driven design of antimicrobial peptides

    Tianyue Ma, Yihan Huang, Hongyu Liu, Wentao Wu, Linxin Ren, Fahad Akhtar, Maryam Nawaz, Zichun Hua, Heng Zheng, Xingzhen Lao

    Discovered via OpenAlex

  110. Intelligent Systems with Applications

    De novo molecular design with agentic AI: Integrating tree search and iterative refinement

    Yukhe Lavinia, Dony Ang, Hagop S. Atamian

    Discovered via OpenAlex

  111. arXiv (Cornell University)

    Predictor-Guided Latent Space Codon Optimization for Maximizing Protein Expression

    Alberto Caron, Tianyu Cui, Dmytro Lituiev, Mangal Prakash, Artem Moskalev, Amina Mollaysa, Bo Zhai, Hirsh Nanda, Daniel M. Poole, Zhongyin Liu, Iman Farasat, Robert C. Davidson, Nikolay V. Manyakov, Tommaso Mansi, Scott Oloff, Rui Jin Liao

    Discovered via OpenAlex

  112. Figshare

    Cross-Kingdom Chimeric Protein Engineering: Concepts, Design Challenges, Validation Strategies, and Opportunities for India

    Quazi Uzaif

    Discovered via OpenAlex

  113. arXiv (Cornell University)

    CODesign: Consistency from Data to Trajectory in All-Atom Protein Binder Co-Design

    Yuanle Mo, Bo Qiang, Haitao Lin, Qinghan Wang, Gang Du, Odin Zhang, Pheng Ann Heng

    Discovered via OpenAlex

  114. Zenodo (CERN European Organization for Nuclear Research)

    D1.3 Protein Engineering Proceeding (Summer schools on Protein Engineering 2026)

    Mária Tomková

    Discovered via OpenAlex

  115. Molecular Cell

    Programming biological behavior with AI-guided de novo protein design

    Philipp Huettemann, Tanja Kortemme

    Discovered via OpenAlex

  116. Green Carbon

    Toward a reduced amino-acid alphabet: AI-guided isoleucine-free ribosomal protein design and its prospective relevance to green biomanufacturing

    Junhong Chen, Jiacheng Huang, Xiaoyan Zhuang, Aihui Zhang

    Discovered via OpenAlex

  117. Cell chemical biology

    Shared α-helix chimeraffibodies enable linker-free bispecific protein design

    Xiaohui Qiu, Xu Chen, Zekai Zeng, Yongxiao Li, Jianye Yuan, Chang Xu, Jiaqi Wang, Xinpei Wang, Ruizhi Lai, Youjian Zhou, 毛景焕, Yiqi Wang, Qiankun Liao, Zhe Wang, Junqing Wang

    Discovered via OpenAlex

  118. ChemRxiv

    Extracting Latent Sequence-Function Information from Directed Evolution to Design Improved C-H Azidases

    Ayantika Ghosh, Sameer D’Costa, Christian A. Gomez, Bryce Johnson, Prajwal Prabhu, Anthony Gitter, Philip A. Romero, Jared C. Lewis

    Discovered via OpenAlex

  119. Current Opinion in Colloid & Interface Science

    Adaptive and Bioresponsive Peptide-Functionalized Lipid-Based Nanocarriers for Precision Nanomedicine

    Basab Kanti Das, Alexandra Iversen, Vijay Kumar Pal, Daniel Aili

    Discovered via OpenAlex

  120. European Heart Journal

    NRP1 interaction with AP2M1 promotes vascular calcification by driving endocytosis of PDGFRβ

    J Cheng, Z Guan, H Chen, A Huang, J Ma, Z Zhang, M Feng, Y Chen, C Xie, H Huang

    Discovered via OpenAlex

  121. Saudi Pharmaceutical Journal

    Snake venom toxins in cancer therapy: advances in targeted delivery and peptide design

    Akmal M. Asrorov, Matluba Mirzaeva, Muzaffar Kayumov, Shamsiddin Fazliddinov, Khamza S. Toshov, Okhunjon Khasanov, Гулнора Гулямовна Рахмонова, Ahmidin Wali, Hayotbek A. Abdullaev, Nurkhodja Mukhamedov

    Discovered via OpenAlex

  122. Nature

    Function-preserving watermarking of AI-generated proteins

    David Stutz, Alexander I. Cowen-Rivers, Guillermo Ortiz-Jiménez, Jeremy D. Ratcliff, Vinícius Zambaldi, Lindsay Willmore, Josh Abramson, Harshnira Hitesh Patani, Christina Kouridi, Florian Stimberg, Mel Vecerík, Alex Chu, Sukhdeep Singh, Sumanth Dathathri, Eliseo Papa, Valentin De Bortoli, Arnaud Doucet B, Demis Hassabis, Jue Wang, Sven Gowal, Pushmeet Kohli

    Discovered via OpenAlex

  123. Protein Science

    Global analysis of thermal and chemical denaturation using CheMelt : Thermodynamic dissection of highly thermostable de novo designed proteins

    Vili Lampinen, Osvaldo Burastero, Iara Plácido Guazzelli, Florian Vogele, Francisca Pinheiro, Jan Stanislaw Nowak, Maria Marta Garcia Alai, Magnus Kjærgaard

    Discovered via OpenAlex

  124. Machine Learning Science and Technology

    From scarce functional labels to label-aware generation in homologous protein families

    Lorenzo Rosset, Martin Weigt, Francesco Zamponi

    Discovered via OpenAlex

  125. Zenodo (CERN European Organization for Nuclear Research)

    De Novo Engineering of pH-Conditional, Cross-Species EGFR Binders via Higher-Dimensional ToposLang and Pharmacological Lattice Quantisation

    Elias Oulad Brahim

    Discovered via OpenAlex

  126. bioRxiv (Cold Spring Harbor Laboratory)

    Repurposing PeTriBERT for Protein–Protein Interaction Prediction with Sequence–Structure Fusion

    Arthur Wavreille, Gabriel Krouk, Baldwin Dumortier

    Discovered via OpenAlex

  127. Insect Molecular Biology

    The anchor and the architect: Merging gene drive, membrane tethering and generative AI for next‐generation vector control

    Yanan Wei, Yanying Sun, Jeong Kyu Bang, Woo Jae Kim

    Discovered via OpenAlex

  128. Current Opinion in Chemical Biology

    What deep learning can and cannot (yet) do for enzyme design

    Judith A. Ahr, Moor M. de Waal, Tudor‐Stefan Cotet, Daniel C. Howell, H. Adrian Bunzel

    Discovered via OpenAlex

  129. Kaggle

    Antimicrobial Peptide Design with ProGen2 and Evolutionary Search

    Rishyanth Reddy, Anukriti Sinha 2312, Eswar Vajja, Shrisha G K

    Discovered via OpenAlex

  130. Kaggle

    GDSBM-AMP: Discrete Schrödinger Bridge for Antibacterial Peptide Design

    Mohsen Dlala, Abdallah Ben Abdallah

    Discovered via OpenAlex

  131. Kaggle

    Antimicrobial peptide design

    Nandini Gantayat

    Discovered via OpenAlex

  132. Research Square

    Memorization in reaction-conditioned generative enzyme design: folding confidence, database identity, and docking all fail to detect it

    Kinsley Torres

    Discovered via OpenAlex

  133. Kaggle

    Antimicrobial peptide design by distribution matching

    Samuel

    Discovered via OpenAlex

  134. Kaggle

    PLM-Guided Masked Resampling for Antimicrobial Peptide Design

    hitwhdata

    Discovered via OpenAlex

  135. Pharmaceuticals

    Mechanisms, Discovery Strategies, and Emerging Opportunities for AI-Assisted Design of Peptides in Cosmetics and Skin Health

    Jiashu Wang, Mustafa Al‐gafari, Parvin Khosravifar, Thomas David Daniel Kazmirchuk, Golshani Ashkan

    Discovered via OpenAlex

  136. Kaggle

    CMD-AMP: Conditioned Masked Discrete Diffusion for Antimicrobial Peptide Design

    Simran Kadadi, Mengbo Wang, shourya10verma, Shyaman

    Discovered via OpenAlex

  137. PLoS Computational Biology

    GeoEPred: A multimodal structure-aware geometric deep learning framework for Gram-negative bacterial secreted effector prediction with sequence semantics

    Shouzhen Song, Hua Wang Shi, Hongfeng Wu, Dachen Liu, Yihang Lin, Nor Ashidi Mat Isa, Quan Zou, Leyi Wei

    Discovered via OpenAlex

  138. bioRxiv (Cold Spring Harbor Laboratory)

    Probing the sequence variability tolerance in a de novo α-helical barrel biocatalyst

    Wael Elaily, M. J. BRAUN, David B. Stoll, Morakot Chakatok, Matteo Aleotti, Birgit Grill, Aleksandar Bijelic, Mélanie Hall, Gustav Oberdorfer

    Discovered via OpenAlex

  139. FEBS Journal

    Toward a minimal amino acid alphabet for protein design

    Karel Půbal, Kseniia Kushnir, Vojtěch Spiwok, Karolína Loužecká, Vladimı́r Setnička, Petra Lipovová

    Discovered via OpenAlex

  140. Scientific Reports

    De novo design of protein antagonists of bacterial pathogen type III secretion system needle assembly

    Ruoqing Jia, Ji Yoon Jung, Aashi Inani, Monneh W Diggs, Evan N. Whitford, Cara N. Dougan, Morgan A. Zitsch, Hongwei Wu, Katherine J. Kenney, Nicolas J. Pizzala, Vicki Hopper Wysocki, Ingeborg Schmidt‐Krey, Andrew C. McShan

    Discovered via OpenAlex

  141. bioRxiv (Cold Spring Harbor Laboratory)

    MIMOSA: Guiding De Novo Antibody Design with Natural Interaction Fingerprints

    Brennan Abanades, Andrea Roncoli, Maniraj Bhagawati, Pan Kessel, Sabine Imhof-Jung, Dominique Doerr, Jonas Schilz, Stefania Vasilaki, Franziska Seeger, Alexandre M. J. J. Bonvin, Richard Bonneau, Vladimir Gligorijević, Anna Vangone

    Discovered via OpenAlex

  142. Frontiers in Cellular and Infection Microbiology

    Lab to codes: multimodel advanced AI-driven pipelines to drive antimicrobial peptide design for the post-antibiotic era

    Naveed Saleem, Emad El-Omar, Naresh Kumar, Mark D. P. Willcox, Xiaotao Jiang

    Discovered via OpenAlex

  143. Current Protein and Peptide Science

    Advances in Antimicrobial Peptides: Design, Mechanism, and Clinical Application-A Critical Review

    Shesham Kumari, Ranjeet Kumar, Manish Singh, Dharmendra Kumar

    Discovered via OpenAlex

  144. Microbial Physiology

    Semi-Rational Design of CpNampt Mutants for Enhanced Nicotinamide Mononucleotide (NMN) Synthesis in Saccharomyces cerevisiae

    yufei Zheng, ting luo, Zhangjun Cao, Zhiwei Huang, Feng Hong, 张兴群

    Discovered via OpenAlex

  145. arXiv (Cornell University)

    From Surfaces to Volumes: Registered Geometry for Protein Representation Learning

    Siyuan Chen, Cai Zhou, Jinrui Zhang, Zhaokang Liang, Taku Komura, Wojciech Matusik, Stephen Bates, Tommi Jaakkola, Wengong Jin, Peter Yichen Chen, Minghao Guo

  146. bioRxiv (Cold Spring Harbor Laboratory)

    De novo design of flexible protein interactions with GuideFlip

    Kai Yi, Qingchao Chen, Dongqi Zhang, Pengfei Tian, Jane L. Wagstaff, Stephen H. McLaughlin, Christopher G. Tate, Kiarash Jamali, Sjors H. W. Scheres

    Discovered via OpenAlex

  147. bioRxiv (Cold Spring Harbor Laboratory)

    AtomWeaver: Multi-Component Flow Matching with a Structured Geometric Prior Facilitates Non-Canonical Peptide Design

    Alexander Kitaygorodsky, David Earl Hostallero, Aron Broom, Elliot Layne, Sungwon Hwang, Ashlin K Kanawaty, Tomáš Babej, Glenn L. Butterfoss, Mark Fingerhuth

    Discovered via OpenAlex

  148. arXiv (Cornell University)

    SPINET: Sheaf Protein Inverse Folding Network

    Jens Lundsgaard, Colin Mikulski, Zhixuan Yan, Dhananjay Bhaskar

    Discovered via OpenAlex

  149. Global Translational Medicine

    Engineering extracellular matrix-mimetic recombinant proteins for stem cell niche and clinical translation

    Jun-Hyeog Jang Jang

    Discovered via OpenAlex

  150. Journal of KIISE

    PoCP: Pareto optimal Cyclic Peptide design with Monte Carlo Tree Guidance

    Taeil Noh, Sanghyun Park

    Discovered via OpenAlex

  151. arXiv (Cornell University)

    AbGaze: Attentive Geometric Representation Learning for End-to-End Antibody Design

    Jiashuo Wang, Siqi Fan, Yu Luo, Zaiqing Nie

    Discovered via OpenAlex

  152. arXiv (Cornell University)

    Mirror-Score: Calibrated, Inference-only Scoring Exposes the Limits of Sequence-compatibility Ranking in D-peptide Design

    Jiada Li

    Discovered via OpenAlex

  153. arXiv (Cornell University)

    LLM sequential decision making under uncertainty in biochemical domains

    Mattias Akke, Soojung Yang, Jurğis Ruža, Sathya Edamadaka, Rafael Gómez‐Bombarelli

    Discovered via OpenAlex

  154. Journal of Medicinal Chemistry

    Design of Wheat Protein-Derived Keap1-Targeting Antioxidant Peptides: Integrating Intelligent Screening, ProteinMPNN-Guided Sequence Optimization, and TAT-Fused Delivery

    Tianfei Yu, Qian Lin, Zheng Sun, Amin Deng, Kai Na, Ting Lu, Li Zhang, Chao Yu, Xiangyu Li, Xiaohua Guo

    Discovered via OpenAlex

  155. arXiv (Cornell University)

    PhiFold: Towards Dynamic Protein Design with Physics-Structured Covariance Modeling

    Yutian Liu, Mujie Lin, LanqianZhang, Meng Fan, Chang Liu, ZhiweiNie, Siwei Ma

    Discovered via OpenAlex

  156. Advanced Computing

    Evaluating Large‐Language Models in Bioinformatics Applications

    Hengchuang Yin, Ziwen Cui, Dongxu Li, Yue Yang, Ying Chang, Xiaobo Zhu, Jun Zhang, Pengwei Hu, Xi Zhou, Lun Hu

    Discovered via OpenAlex

  157. Science Advances

    A designed ubiquitin-binding protein selectively enriches and visualizes unanchored ubiquitin

    Shihua Shi, Alexandra M. Bendel, Georg Kempf, Jacint Sanchez, Sohei Majima, Vytautas Iešmantavičius, Daniel Heß, Jan Seebacher, Yong Huang, Sucheta Ghosh, Cao Chun, Gabriele Matthias, Jeffrey W. Bode, Yohei Yamauchi, Guillaume Diss, Patrick Matthias, Longlong Wang

    Discovered via OpenAlex

  158. Small Structures

    Modular Metalloprotein Nanowires With Semiconductor‐Scale Conductivity and Tunable Redox Behavior

    Nga T. Lam, Lorenzo Travaglini, Yun X. Chen, Dominic J. Glover

    Discovered via OpenAlex

  159. bioRxiv (Cold Spring Harbor Laboratory)

    Predicting single mutation effects on binding affinity at protein-protein interfaces based on MMPBSA calculations

    Jakob Noske, Thibaud Lepoivre, Maxim Janzen, Birte Höcker

    Discovered via OpenAlex

  160. arXiv (Cornell University)

    Spectral Feedback for Test-Time Alignment of Protein Diffusion Models

    Shai Dickman, Mert Cemri, Landon Butler, Kannan Ramchandran

    Discovered via OpenAlex

  161. bioRxiv (Cold Spring Harbor Laboratory)

    PepSpace: An Automated, Physics-Driven Directed Evolution Platform for the De Novo Design of Specific Peptide Binders and Condensate Modulators

    J. Oller-Iscar, Andrés R. Tejedor, Alejandro Feito, María Velasco‐Estevez, Alberto Ocaña, Rosana Collepardo‐Guevara, Jorge Reñe Espinosa

    Discovered via OpenAlex

  162. Organic Letters

    Artificial Enzyme Design with an Abiological Salicylaldehyde Site Enables Biocatalytic Activation of Glycine Esters

    Yuhui Sheng, Zhi Zhou

    Discovered via OpenAlex

  163. Zenodo (CERN European Organization for Nuclear Research)

    Fitting Boundary Detection: A Navigation Methodology for AI Systems from Closed-Set Fitting to New Knowledge Generation

    GenMin Li

    Discovered via OpenAlex

  164. bioRxiv (Cold Spring Harbor Laboratory)

    Protein Language Models: Learning From Evolution, Designing Beyond It

    Maurice Brenner, Julius Schlensok, Alexander P., Robert Schmirler, Michael Heinzinger

    Discovered via OpenAlex

  165. bioRxiv (Cold Spring Harbor Laboratory)

    SurfGraphPro: Integrating Protein Language Models with Geometric Deep Learning On Coarse Protein Surfaces for Binding Site Prediction

    Adela Habib, Li‐Wei Hung, Martha Dix, Kaetlyn Gibson, P.S. Chain, Bin Hu

    Discovered via OpenAlex

  166. bioRxiv (Cold Spring Harbor Laboratory)

    Boltz2-Notebook: An Interactive Google Colab Platform for Diffusion-Based Biomolecular Structure and Binding Affinity Prediction using the Boltz2 model

    Atharva Tilewale, Dhaval Patel

    Discovered via OpenAlex

  167. bioRxiv (Cold Spring Harbor Laboratory)

    Agentic campaign control for high-throughput de novo binder design

    Minkyu Jeon, Jinyeop Song, Jina Kim, Ellen D. Zhong

    Discovered via OpenAlex

  168. ACS Synthetic Biology

    Effective Sequence-to-Expression Prediction for a Model Membrane Protein Using Machine Learning and Computational Protein Design

    Yuxin Shen, Maddie Lewis, Juno Underhill, Adrian John Mulholland, Diego A. Oyarzún, Paul Curnow

    Discovered via OpenAlex

  169. Zenodo (CERN European Organization for Nuclear Research)

    An Automated Computational Factory for High-Confidence De Novo Protein Design: Multi-Temperature Sequence Design with Physics-Based Validation

    陈世强

    Discovered via OpenAlex

  170. Journal of Biomolecular Structure and Dynamics

    Design of a high-affinity IL-21 decoy receptor as a novel therapeutic strategy for autoimmune disorders

    Sara Vazifeshenas, Zahra Hajihassan, Seyed Shahriar Arab, Ali Najafyar

    Discovered via OpenAlex

  171. Catalysis Reviews

    AI-Assisted rational enzyme engineering: advancing biocatalysis for industrial applications

    Muhammad Shafiq, Liaqat Zeb, Xiang Wang, Chen Wang, Yi He, Huasong Luo, Muhammad Ayaz, Bin Xue, Yanjun Wan, Wen Zhang, Xianheng Song, Yuan Yuan, Shuyun Ju, Yajun Wang

    Discovered via OpenAlex

  172. bioRxiv (Cold Spring Harbor Laboratory)

    NoroScope: Exploring the Mutational Landscape of the Human Norovirus Capsid Protein with Context-Aware Machine Learning

    Sebastian Bowyer, David James Allen, Nicholas Furnham

    Discovered via OpenAlex

  173. ChemistrySelect

    Template‐Derived Engineering of Peptide Inhibitors Targeting HSP90–CDC37 Interface: A Theoretical Framework for Cancer Therapeutics

    Sarath Perumal, K. Ramanathan

    Discovered via OpenAlex

  174. ACS Synthetic Biology

    Balancing Precursor Supply and Enhancing Enzyme Solubility for Efficient Production of ( S )-Reticuline in Escherichia coli

    Xiaxia Zhang, Muhammad Hassan Butt, Wen Zhang, Yuan Gao, Shibo Guo, Jianfeng Fang, Xiaolin Shen, Jia Wang, Xinxiao Sun, Qipeng Yuan

    Discovered via OpenAlex

  175. bioRxiv (Cold Spring Harbor Laboratory)

    De novo design of protease-activatable cytokine prodrugs

    Hojeong Shin, Julissa G. Tello, Chan Johng Kim, Jung-Ho Chun, Frank Peprah, Brendan D. Parent, Tavus Atajanova, Robiah Arefin Ibn Mahmud, Li Qiang, Andrew J. Aguirre, Stephanie K. Dougan, Michael Lawrence Dougan, David A. Baker

  176. Nature Communications

    Generative AI designs functional thiolation domains for reprogramming non-ribosomal peptide synthetases

    Emre Fatih Bülbül, Seounggun Bang, Kevin George, Gabriele Bianchi, Prateek Raj, Seonyong Chung, Vincent Pauline, Ramon Hochstrasser, Hannah A. Minas, Walid A. M. Elgaher, Andreas M. Kany, Anna K. H. Hirsch, Steven Schmitt, Dirk W. Heinz, Olga V. Kalinina, Dietrich Klakow, Kenan A. J. Bozhüyük

    Discovered via OpenAlex

  177. Nature Computational Science

    Intuitive enzyme design with LLM agents

    Terra Sztain

    Discovered via OpenAlex

  178. ChemRxiv

    Machine Learned Interatomic Forces as Inference-Time Physical Guidance for All-Atom Diffusion Peptide Design

    Biao Zeng, Youyi Song, Jinfeng Liu

    Discovered via OpenAlex

  179. Preprints.org

    Two-Stage Solubility Optimization of an Anti-VirB4 Nanobody: From Rational Mutagenesis to AI-Driven De Novo Design of a Single-Domain Antibody Macromolecule

    Guotao Pan, 张耀新, 周欢敏, Fan Yang, Lina Hou, Pei Gong, Fang Wan

    Discovered via OpenAlex

  180. UF Journal of Undergraduate Research

    AI Protein Design of N-Acetylgalactosamine Deacetylase for Universal Blood Type Conversion

    Nicholas Marotta, Alberto Pérez

    Discovered via OpenAlex

  181. Protein Science

    Engineering a protein homodimer from a heterodimer: A chimeric DBHS protein

    Andrew C. Marshall, Isabelle Mohnen, Alejandro Villa Gomez, Archa H. Fox, Gavin J. Knott, Charles S. Bond

    Discovered via OpenAlex

  182. Nature Communications

    Generating protein hydrogels with customizable stress relaxation behavior via deep learning-driven entanglement design

    Puqing Deng, Yutong Wu, Hong Kiu Francis Fok, Linyan Li, Wenbin Zhang, Fei Sun, Hanyu Gao

    Discovered via OpenAlex

  183. ACS Medicinal Chemistry Letters

    Antibody Hotspot-Centric de Novo Design of Peptide Inhibitors of Influenza A Virus Membrane Fusion

    Rameshwar U. Kadam, Jarek Juraszek, Davide Branduardi, Jeroenvan Ameijde, Divita Garg, Jan Vermond, Mandy A. C. Jongeneelen, Chan Tang, Ronald Vogels, Maria J. P. van Dongen, Boerries Brandenburg, Robert H. E. Friesen, Ian A. Wilson

    Discovered via OpenAlex

  184. Journal of Agricultural and Food Chemistry

    Integrated Transporter Engineering and Semi-Rational Enzyme Design in Corynebacterium glutamicum for High-Level Natural Blue Pigment Indigoidine Production

    Junjie Sun, Hui Gao, Xinyang Xu, Shougang Wang, Meijuan Xu

    Discovered via OpenAlex

  185. International Journal of Molecular Sciences

    Anisotropic Gold Nanoconjugates Bearing Immunoinformatically Designed T-Cell Epitope-Containing Peptides: Comparative Evaluation in THP-1 and Human Primary Macrophages

    Braulio Contreras-Trigo, Enrique Guzmán-Gutiérrez, Eduardo Zúñiga, Fabián Sáez-Ahumada, Víctor Fica-León, Simón Guerrero, Dariela Núñez, Andrea Sánchez, Carmen Molina-Parı́s, Boštjan Kobe, Victor Manuel Díaz-García, Patricio Oyarzún

    Discovered via OpenAlex

  186. Preprints.org

    AF-RECAL: Multi-Modal Structural Recalibration of AlphaFold 3 Hallucinations in Intrinsically Disordered Human Disease Targets

    Mudit Sharma

    Discovered via OpenAlex

  187. Journal of Chemical Information and Modeling

    REAPS: An All-Atom Receptor-Aware Geometric Deep Learning Framework for De Novo Design of Linear and Macrocyclic Peptide Binders

    Yongkang Qiu, Jingxin Qiao, Lengjing Zhu, Le Du, Shengyong Yang, Jun Zou

    Discovered via OpenAlex

  188. Molecules

    Anticancer Peptides: Design Principles, Translational Bottlenecks, and Emerging Opportunities

    Marissa E. Di, Y. Peter Di

    Discovered via OpenAlex

  189. Angewandte Chemie International Edition

    De Novo Design and Structural Optimization of Mn(salen)‐Based Artificial Metalloenzymes for Asymmetric Sulfoxidation

    Jingxiang Wang, Yunling Deng, Indrek Kalvet, Amira Haque, Huiguang Dai, David A. Baker, Yi Lu

  190. FEBS Letters

    Prospecting the protein design landscape

    Jakob R. Riccabona, Katharina T. Stonig, Jens Meiler, Clara T. Schoeder, Monica L. Fernández‐Quintero

    Discovered via OpenAlex

  191. bioRxiv (Cold Spring Harbor Laboratory)

    Controlled Blood-Brain Barrier Modulation by a High-Affinity Claudin-5 Peptide Binder

    Alessandro Berselli, Martina Trevisani, Giulio Alberini, Aldo Pastore, Andrea Di Fonzo, Andrea Armirotti, Valentina Castagnola, Luca Maragliano, Fabio Benfenati

    Discovered via OpenAlex

  192. Journal of Structural Biology X

    Evolutionary and structural pathways of antibody maturation reveal principles for engineering potent SARS-CoV-2 neutralizers

    Muhammad Waqas Nasir, QIyun Liang, Jing Wang, Yan Sun, Xiangyu Zhang, Rishen Liang, Jun He, Umer Rashid, Jiabing Wu, Yong Gao

    Discovered via OpenAlex

  193. bioRxiv (Cold Spring Harbor Laboratory)

    Computational design of potent, broadly neutralizing anti-Nipah virus and Hendra virus miniproteins

    Jeremiah Nelson Sims, Risako Gen, Kaitlin R. Sprouse, Young‐Jun Park, Zhaoqian Wang, Moushimi Amaya, Alka Jays, Brendan Larsen, Cameron Stewart, Jack T Brown, Robert J. Ragotte, Rashmi Ravichandran, Garrett Ruth, Xinting Li, Dionne K. Vafeados, Jesse D. Bloom, Christopher C. Broder, David Veesler, David A. Baker

  194. ACS Chemical Neuroscience

    XL-MS and De Novo Protein Design Identified a Common Motif for TREM2 Binding

    Doniesha Perera, Emmanuel Gboyega Ajiboye, Kalana Pitakatuwana, Sophia Wier, Vincent Duong, Haifan Wu

    Discovered via OpenAlex

  195. Journal of Chemical Information and Modeling

    Explainable Artificial Intelligence to Unveil Patterns of Antioxidant Peptides for Free Radical Regulation

    Maria Carolina J. A. Schneider, Bárbara Saraiva Souza, Leonardo Vasconcelos Ferreira, Marina Geisiely Damaso, André Silva Pimentel

    Discovered via OpenAlex

  196. Journal of Chemical Information and Modeling

    Diff-SelfA-PepGSI: A Diffusion-Based Framework for De Novo Generation, Screening, and Morphological Identification of Self-Assembled Peptide Sequences

    Weizhong Sun, Yuning Ma, Xiumin Shi, Mingshan Wei, Ao He, Weizhi Wang

    Discovered via OpenAlex

  197. UNC Libraries

    From Protein Design to the Energy Landscape of a Cold Unfolding Protein

    Edward H. Snell, Brian A. Kuhlman, Lakshmanane Premkumar, A E Garcia, Thomas M Weiss, Surya V. S. R. K. Pulavarti, Joseph S. Harrison, Jermel R. Griffin, Thomas Szyperski, Edward A. Esposito, George I. Makhatadze, Jack B. Maguire, Shirley Yuen

    Discovered via OpenAlex

  198. Journal of Agricultural and Food Chemistry

    Artificial Intelligence-Aided De Novo Design of High-Affinity Protein Binders Against Shiga Toxin 2

    Xianglin Zhao, Xiao Feng, Huaixia Li, Menghui Wang, Tingting Feng, Huixia Zhan, Jiaying Tang, Shaowen Li, Tingting Li, James Connolly, Rui Zhou, Qi Huang

    Discovered via OpenAlex

  199. Journal of Proteome Research

    Development of a Translational Assay for Identification and Quantitation of Orthologous Proteins to Aid Drug Development in Preclinical Models

    Blandine Rougemont, Julie Borgel, Zoe Walker, Irene Zubiri, ronan.ocualain not provided, Neda Ali Mohammadi Nafchi, Christopher E. Shaw, Ernestas Sirka, John Isaac, Carlos J. Miranda, Anna Ettorre

    Discovered via OpenAlex

  200. bioRxiv (Cold Spring Harbor Laboratory)

    Machine learned potentials with electrostatic embedding accurately capture Kemp eliminase reactivity

    Abbie Lear, Elliot W. Chan, Kirill Zinovjev, Marc W. van der Kamp, H. Adrian Bunzel, Adrian John Mulholland

    Discovered via OpenAlex

  201. bioRxiv (Cold Spring Harbor Laboratory)

    A Turing-Style Test for In-Silico Antibodies: How Sampling Mode Makes WGAN-GP Beat VAE in the Wet Lab

    Arkadij Kummer, Farbod Mahmoudinobar, Wendi Liu, J. Wade Davis, Eric J. Ma, Sandeep Kumar

    Discovered via OpenAlex

  202. Cell Systems

    Sampling protein language models for functional protein design

    Jeremie Theddy Darmawan, Yarin Gal, Pascal Notin

    Discovered via OpenAlex

  203. Angewandte Chemie International Edition

    In Vitro Selection of Functional Neoproteins Containing Highly Fluorinated Cores

    Adam T. Beattie, Alexander A. Vinogradov, Chikako Okada, Toru Sengoku, Takayuki Katoh, Hiroaki Suga

    Discovered via OpenAlex

  204. bioRxiv (Cold Spring Harbor Laboratory)

    Multistate Enzyme Design Enables Efficient and Stereoselective Multistep Catalysis

    N. T. Hang Pham, Rui Guo, Rosalinda P Garcia Jimenez, Amy E. Hutton, Linus O. Johannissen, Johann A Wehrstedt, Behnoush Seifinoferest, Zachary Birch-Price, Jordan Berreur, Sam Hay, Michael C. Thompson, Anthony P. Green, Roberto A. Chica

    Discovered via OpenAlex

  205. arXiv (Cornell University)

    OpenAI4S: Code as Action, Science as Sessions

    Gongbo Zhang, Hao Li, Yu Wang, Mujie Lin, Liuzhenghao Lv, Yicheng Mao, Yimi Wang, Jun Zhu, Minhan Tang, Zhengxiang Jiang, Yusong Wang, Jiayu Yao, Kunpeng Ning, Dawei Pang, Yonghong Tian, OpenAI4S Community, Yuyang Liu, li Yuan

    Discovered via OpenAlex

  206. ACS Sustainable Chemistry & Engineering

    MPNN-Guided Redesign of PET Hydrolases with Enhanced Catalytic Activity below the PET Glass Transition Temperature

    Aransa Griñén, Valeria Eltit-Villarroel, Francisca Durán-Osorio, Javiera A Avilés, Flavia C. M. Zacconi, Edson Norberto Carcamo-Noriega, Christopher D. Bahl, Ben A. Meinen, César A. Ramírez‐Sarmiento

    Discovered via OpenAlex

  207. UNC Libraries

    Aminoacyl-tRNA synthetase urzymes optimized by deep learning behave as a quasispecies

    Henry Dieckhaus, Brian A. Kuhlman, Peter R. Wills, Jordan Douglas, Laurie Betts, Charles W Carter, Sourav Kumar Patra, Nicholas Z. Randolph

    Discovered via OpenAlex

  208. Nature Communications

    Discovery of an antagonist nanobody targeting the oxytocin receptor with tocolytic effect in mice

    Jia Nie, Kaixuan Gao, Xin Zhang, Hengyu Meng, Qi Li, Xiaowen Zhang, Yanying Wu, Hongtao Zeng, Wan'er Liu, Lijuan Liu, Lunbo Tan, Xiaoou Sun, Xiangyu Liu, Weishe Zhang

    Discovered via OpenAlex

  209. Molecular Catalysis

    Multidrug resistance regulators (MDRs) as emerging scaffolds for artificial enzyme design

    Mingye Zhao, Jie Chen, Xianglei Fu, Xing Zhang, Xiahui Xiong

    Discovered via OpenAlex

  210. Engineering Microbiology

    Systematic optimization of Komagataella phaffii (Pichia pastoris) for high-efficiency recombinant protein production: Advancements in strain engineering, fermentation optimization, and AI-driven technologies

    Yue Huang, Jialiang Wang, Aoxue Wang, Liqi Zheng, Ying Lin, Shuli Liang

    Discovered via OpenAlex

  211. bioRxiv (Cold Spring Harbor Laboratory)

    Chemical Descriptors and Deep Learning Embeddings for Scoring de novo Peptide Designs

    Quentin Trolliet, Alex Abrudan, Aryan Bhasin, Yunguan Fu, Joao Paulo Euko, Cheng Zhang, Francesco Saccon

    Discovered via OpenAlex

  212. bioRxiv (Cold Spring Harbor Laboratory)

    De novo design of allosterically controlled enzymes

    Alex Shida, Kelly Wang, Hojae Choi, Samuel J. Pellock, Adam J. Broerman, Saman Salike, William S. Grubbe, Emily Joyce, Alex Kang, Asim K. Bera, Xinting Li, Arvind S. Pillai, David A. Baker

  213. Frontiers in Food Science and Technology

    A design science framework for alternative proteins: coupling ingredient functionality, processing physics, and predictive modeling

    Gülsün Akdemir Evrendilek

    Discovered via OpenAlex

  214. Journal of Chemical Information and Modeling

    Closed-Loop Multi-Objective Optimization for Receptor-Selective Cell-Penetrating Peptide Design

    Iori Yamahata, Hidetomo Yokoo, Yosuke Demizu, Teppei Shimamura, Shuto Hayashi

    Discovered via OpenAlex

  215. bioRxiv (Cold Spring Harbor Laboratory)

    EnZight: A Structure-Guided Algorithm to Identify and Prioritize Substitution Hotspots for Enzyme Engineering

    Rune Rahbek Oestergaard, Mikkel Lyskjær Jensen, Suzana Siebenhaar, Deniz Bicer, Peter Wad Sackett, Alexander Andersen, Matteo Tiberti, Elena Papaleo, Serina L. Robinson, Søren Thirup, Peter Westh, Laura Rotilio, Jens Preben Morth

    Discovered via OpenAlex

  216. Nature Computational Science

    MutexaGPT: an intuition-to-design translator for physics-based enzyme engineering

    Qianzhen Shao, Yinjie Zhong, Sebastian L. Stull, Xinchun Ran, Ning Ding, Kieran Nehil-Puleo, Ruizhe Yao, Han Xu, Zhongyue John Yang

    Discovered via OpenAlex

  217. Nature Biomedical Engineering

    Sequence and structural determinants of efficacious de novo chimaeric antigen receptors

    Arthur Chow, Hoyin Chu, Ruofan Li, Benan N. Nalbant, Abdul Vehab Dozic, Laura C. Kida, Zeyu Tang, Joseph R. Palmeri, Caleb A. Lareau

    Discovered via OpenAlex

  218. Journal of Chemical Information and Modeling

    Mechanism-Guided Antimicrobial Peptide Design through Membrane-Surface Fingerprinting and Graph Diffusion

    Zhenyu Ma, Sixin Tian, Mengmeng Sheng, Hong Cheng, Jingyi Zhu, Chunyi Yang, Limei Xu, Min Xiao, Jian Li, Yanyan Li, Xukai Jiang

    Discovered via OpenAlex

  219. ChemRxiv

    Data-driven strategies for enzyme engineering: From machine learning to protein language models

    Shaozhen Ding, Peng Wu, Shubo Li, Yuxuan Yang, Han Zhu, Heng Yu, Yu Tian, Dachuan Zhang, Qian‐Nan Hu

    Discovered via OpenAlex

  220. bioRxiv (Cold Spring Harbor Laboratory)

    Specificity-driven protein binder design with Odin-Multi

    Valentas Brasas, Charlotte Risager Christensen, Kasper Haldrup Björnsson, Victor Emil Møller, Beatrice Scapolo, Melisa Benard-Valle, Mads Mørup Nygaard, Jens Christian Nielsen, Sine Reker Hadrup, Kristoffer H. Johansen, Timothy P. Jenkins

    Discovered via OpenAlex

  221. bioRxiv (Cold Spring Harbor Laboratory)

    De novo Rubisco design with protein language models

    Alexander J. Kehl, Simon K. S. Chu, Jose Henrique Pereira, Jennifer Lee, Renée Z. Wang, Michael Gigl, Paul D. Adams, Patrick M. Shih, Justin B. Siegel

    Discovered via OpenAlex

  222. bioRxiv (Cold Spring Harbor Laboratory)

    Empirical Geometry-Guided Modeling Enables Robust, High-Throughput Collagen Structure Prediction

    Bruno Howard, Maxwell Bauer, Markus J. Buehler

    Discovered via OpenAlex

  223. Colloids and Surfaces B Biointerfaces

    Programmable crosslinking strategies for the rational design of engineered protein hydrogels

    Tingyu Xu, Jia Wei, Zihan Zhang, Haonan Xia, Shengwang Zhou

    Discovered via OpenAlex

  224. Research Square

    Joint optimisation of amino acid and coding sequence for de novo designed proteins

    Anees Ahmed Mahaboob Ali, Radhakrishnan Delhibabu, Everette Jacob Remington Nelson

    Discovered via OpenAlex

  225. bioRxiv (Cold Spring Harbor Laboratory)

    Protein Design Viz (PDV): lightweight protein structure visualization studio with validated quantitative analytics and antibody-specific toolkit

    Konrad Krawczyk, Paweł Dudzic, Sandeep Kumar

    Discovered via OpenAlex

  226. bioRxiv (Cold Spring Harbor Laboratory)

    RFOptimization: Guiding Design Optimization with All-Atom Structure Prediction

    Odin Zhang, Jiaqi Wang, Tuscan Rock Thompson, Ziyi You, Zihao Song, Frank DiMaio, David A. Baker

  227. Machine Learning Health

    Advancing knotted protein design with ESM3: guided generation and topological insights

    Eva Marsalkova, Petr Šimeček

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 5.4 Transformer-based · 5.Function to Sequence

  228. Exploration of Drug Science

    Flagellar pocket receptors as entry point for protein-based drugs against kinetoplastid parasites

    Lucila Attala, Cecilia Vernetti, Elvio Rodríguez Araya

    Discovered via OpenAlex

  229. bioRxiv (Cold Spring Harbor Laboratory)

    Inverse FoldDir: Structure-conditioned Protein Sequence Design by Dirichlet Flow Matching

    Alp Tartici, Mihajlo Stojković, Anru Tian, Michael C. Jewett, Russ Biagio Altman, Bruce J. Wittmann

    Discovered via OpenAlex

  230. bioRxiv (Cold Spring Harbor Laboratory)

    De Novo Design and AlphaFold3 Evaluation of Protein Binders Targeting Specific Sites of MAP4K4

    Aarnav Jain, Alexander V. Tobias

    Discovered via OpenAlex

  231. arXiv (Cornell University)

    Agentic BAIM-LLM Evaluation (ABLE): Benchmarking LLM Use of Protein Design Tools

    Bryce Cai, Geetha Jeyapragasan, Samira Nedungadi, Jake Yukich, Seth Donoughe

    Discovered via OpenAlex

  232. Food Research International Translational Research

    Molecular engineering of single-cell proteins for precision functional food design: Linking cellular architecture, protein structure, digestibility, and techno-functional performance

    Gebeyehu Ayele, Habtamu Admassu, Gadissa Mosisa, Abebe Desalegn, Molla Abeje

    Discovered via OpenAlex

  233. ACS Omega

    Evolutionary Dynamics-Aware De Novo Design of a Thermostable NS1-Derived Diagnostic Protein for Yellow Fever Virus

    Junior Olímpio Martins, Patrícia da Silva Antunes, Rodrigo Lopes Sanz Duro, Robert Andreata‐Santos, Clara Lacerda de Athayde, Gustavo Cabral‐Miranda, Luiz Mário Janini, Franca Fraternali, Carlos Henrique Bezerra da Cruz, Ricardo Durães‐Carvalho

    Discovered via OpenAlex

  234. Journal of the American Chemical Society

    CatESO: Differentiable Enzyme Sequence Optimization Guided by Substrate-Aware K cat Prediction

    Zhenjia Gan, Yuzhi Xu, Junde Xu, Zhihao Wu, Juping Huang, Jiabin Yin, Guangyong Chen, John Z. H. Zhang

    Discovered via OpenAlex

  235. bioRxiv (Cold Spring Harbor Laboratory)

    BAGEL-CAR: Reflections on the Bits to Binders Competition

    Jakub Lála, Stefano Angioletti‐Uberti

    Discovered via OpenAlex

  236. Biochemical Journal

    Graph-based representations in modern protein science

    Dana S. Matthews, Sacha B. Pulsford, Anthony Brancewicz, John Z. Chen, Barnabas Gall, Mahakaran Sandhu, Matthew A. Spence, Colin J. Jackson

    Discovered via OpenAlex

  237. Nucleic Acids Research

    ProRB: a structure-free unified framework for joint prediction and design of protein–RNA interactions

    Yiming Xue, Xiaojian Liu, Weimin Zhu, Shengfan Wang, Hong‐Bin Shen, Xiaoyong Pan

    Discovered via OpenAlex

  238. bioRxiv (Cold Spring Harbor Laboratory)

    De novo designed single-domain antibodies protect against lethal cobra venom neurotoxicity in vivo

    Max D. Overath, Emil V. S. Lundquist, Kasper Haldrup Björnsson, Samuel R Kerwin, Christian P. Jacobsen, Mark von Bülow Møiniche, Diego Ruiz Espi, Kim Boddum, Melisa Bénard-Valle, Monica L. Fernández‐Quintero, Stephen P. Mackessy, Timothy P. Jenkins

    Discovered via OpenAlex

  239. bioRxiv (Cold Spring Harbor Laboratory)

    De novo design of CR2 binder as vaccine scaffold

    Yuan‐Tao Liu, Yi-Na Yin, Hui-Qin Xu, Wen-Ting Du, Chu Xie, Ping Wu, Hang Zhou, Bing-Zhen Cheng, Guo‐Long Bu, Guo‐Kai Feng, Qian Zhong, Zheng Liu, Mu‐Sheng Zeng, Cong Sun

    Discovered via OpenAlex

  240. bioRxiv (Cold Spring Harbor Laboratory)

    De novo design of ligand binding proteins using large language models alone

    Nam Hyeong Kim, A. Katherine Hatstat, Hyunil Jo, Yibing Wu, William F. DeGrado

    Discovered via OpenAlex

  241. arXiv (Cornell University)

    SimpleDesign: A Joint Model for Protein Sequence and Structure Codesign

    Jiarui Lu, Yuyang Wang, Yizhe Zhang, Jiatao Gu, Navdeep Jaitly, Joshua M. Susskind, Miguel Ángel Bautista

    Discovered via OpenAlex

  242. PubMed Central

    The physical foundation beneath protein generative modeling

    Tianyu Lu, Po‐Ssu Huang

    Discovered via OpenAlex

  243. bioRxiv (Cold Spring Harbor Laboratory)

    High-dimensional HIV-1 quasispecies modeling guides escape-proof antibody design

    Griffin Kutler Dodd, Paulien Hogeweg, Rob J. de Boer

    Discovered via OpenAlex

  244. bioRxiv (Cold Spring Harbor Laboratory)

    Comprehensive Evaluation of Protein Language Model Embeddings for Drug–Target Affinity Prediction

    Matija Marijan, Ivan Tanasijević

    Discovered via OpenAlex

  245. Scientific Reports

    Non-standard proteins in the lens of AlphaFold 3: a case study of amyloids

    Alicja W. Wojciechowska, Jakub Wiktor Wojciechowski, Gert Vriend, Małgorzata Kotulska

    Discovered via OpenAlex

  246. Nature

    Creating bottom-up RNA transfer vehicles from synthetic protein assemblies

    Maren Kirstin Schuhmacher, Christoph Gruber, Christopher M. R. Lang, Ricardo Ruijpers, Lyupka Mazneykova, Brice Beinsteiner, Ariane Krus, Barbara Tremmel, Friederike Reinhardt, Karoline Kadletz, Zhe Ma, Lucie Casalta, Josep M. Cambra, Dina Yehia Otify, Iolo Balken, Leon Hetzel, Juliane Merl‐Pham, Tatjana Dorn, Marina Luchner, Lea Bauersachs, K. Ganea, Natascha Wieser, Alexander Emrich, Emirhan Yağmur, Katrin Rager, Gauhar Sagindykova, Niklas Armbrust, Julian Geilenkeuser, Gil G. Westmeyer, Elvir Bećirović, Martin Biel, Rouzanna Istvánffy, Daniela M. Vogt Weisenhorn, Dong‐Jiunn Jeffery Truong, Fabian Joachim Theis, Gregor Ebert, Alessandra Moretti, Ali Ertürk, Andrea Bähr, Christian Kupatt, Marion Jasnin, Nikolai Klymiuk, Florian Giesert, Wolfgang Wurst

    Discovered via OpenAlex

  247. Journal of Enzyme Inhibition and Medicinal Chemistry

    Design of aptamer peptides for immunomodulation

    Arpan Chowdhury, Prajesh Shrestha, Subramanian Vivekanandan, Venkatesh Mayandi, Mukesh Mahajan, Seetharama D. S. Jois

    Discovered via OpenAlex

  248. Antibodies

    The Evolution of Artificial Intelligence in Antibody Design: From Structure-Based Engineering to Generative Models

    Ida Szataniak, Kacper Packi

    Discovered via OpenAlex

  249. Zenodo (CERN European Organization for Nuclear Research)

    Dissecting the limitations of AlphaFold3 confidence metrics for de novo antibody design selection

    anonymous

    Discovered via OpenAlex

  250. DOAJ (DOAJ: Directory of Open Access Journals)

    AI-driven innovation and applications in crop breeding technology

    Shunmei LI, Jingyi XU, Ruiying LIU, Cuirong Tan, Qinlong Zhu, Yongyao XIE

    Discovered via OpenAlex

  251. arXiv (Cornell University)

    SymFold: Synergizing Evolutionary and Structural Priors for Accurate Protein Inverse Folding

    Handong Wang, Jiaxin Qi, Baisheng Lai, Jianqiang Huang

    Discovered via OpenAlex

  252. International Journal of Biological Macromolecules

    Extremozymes for food fermentation: Integrating AI, metagenomics, and protein engineering

    Subuhi Kashif Ansari, Nusrat Hamid Shah, Noureddine Elboughdiri, Anis Ahmad Chaudhary, Mohamed A. M. Ali, Atif Khurshid Wani

    Discovered via OpenAlex

  253. Briefings in Bioinformatics

    EquiDesign: a versatile computational framework for de novo protein sequence design

    Qiang Gao, Zhongyu Xu, Kai Chen, Xiaochen Cen, Ke Yan, Jinxin Liu, Zhiwei Ji

    Discovered via OpenAlex

  254. Chemical Reviews

    Computational Platforms for Membrane-Active Peptide Therapeutic Design

    Bing Zan, Charles H. Chen, Mehwish Sabha, Ke Wu, Mahnoor Kadri, Oluebube L. Nwajiaku, Dominique Hoogland, Jakob P. Ulmschneider, Martin B. Ulmschneider

    Discovered via OpenAlex

  255. Swarm and Evolutionary Computation

    A surrogate-assisted multi-objective optimization algorithm for antibody design with multi-source datasets

    Ziyang Shi, Xinyi Xu, Haotian Zhang, Shenghan Ren, Handing Wang

    Discovered via OpenAlex

  256. Annals of Esophagus

    Tumor microenvironment-directed novel checkpoint strategies in esophageal squamous cell carcinoma: a narrative review on current status and limitations

    Chien-Huai Chuang, Jhe-Cyuan Guo, Chih-Hung Hsu

    Discovered via OpenAlex

  257. Wiley Interdisciplinary Reviews Computational Molecular Science

    Deep Learning for Protein Modeling: From Single Structure to Bound Complex and Thermodynamic Ensemble, With a Focus on Architectural Design

    Daniele Angioletti, Matteo Carli, Marco Nobile, Vittorio Limongelli

    Discovered via OpenAlex

  258. University of Liverpool

    Efficient matching of predicted protein structures into high to intermediate resolution CryoEM maps with Slice’N’Dice and ABCFold

    Luc G. Elliott

    Discovered via OpenAlex

  259. Briefings in Bioinformatics

    Surf2Spot: a surface-informed geometry-aware model for predicting partner-independent binder and nanobody design hotspots

    Anwen Zhao, Yu Li, Zixuan Wang, Tianhao Wu, Ran Fu, Yuxuan Lou, Yanfen Xu, Xuliang Han, Wenying Wang, Jun Yan, Xiangfeng Wang

    Discovered via OpenAlex

  260. Bioinformatics

    Design of peptides with noncanonical amino acids using flow matching

    Jin Sub Lee, Philip M. Kim

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.8 Flow-based

  261. Comprehensive Reviews in Food Science and Food Safety

    Upcycling Vegetable Waste Into Functional Food Ingredients via Synergistic Microbial Engineering and Artificial Intelligence

    Jiajin Sun, Dongbo Ma, Qingwei Meng, Chongpeng Bi, Jianping Li, Anshan Shan

    Discovered via OpenAlex

  262. Research Square

    Benchmarking unsupervised protein mutational effect predictors: practical guidelines for protein engineering and reduced accuracy at beneficial residues

    Teppei Deguchi, Yoichi Kurumida, Kaito Kobayashi, Yutaka Saito

    Discovered via OpenAlex

  263. Zenodo (CERN European Organization for Nuclear Research)

    An AI-Designed Lysosomal Degradation System Targeting HIV-1 Reverse Transcriptase: A New Strategy for Achieving Functional Cure

    Ao Li

    Discovered via OpenAlex

  264. Trends in Biochemical Sciences

    Minimal-alphabet proteins by evolution, engineering, and design

    Filip Buchel, Valerio Guido Giacobelli, Klára Hlouchová

    Discovered via OpenAlex

  265. Journal of Chemical Information and Modeling

    SA-MPNN: A Sequence-Aware ThermoMPNN for Accurate Prediction of Mutational Effects on Protein Thermodynamic Stability

    Xin Yue Zhang, Xiang Zheng, Ze Yuan Dong, Jing Xiao, Hao Zhang, Min Cong Wu, Zhao Ming Liu, Guo Hui Li, Jiao Li, Wei Bu Wang, Yu Liang, Qi Ming Li, Ji Guo Su

    Discovered via OpenAlex

  266. Science Advances

    Programmable protein degraders enable selective knockdown of pathogenic β-catenin subpopulations in vitro and in vivo

    Tianzheng Ye, Azmain Alamgir, Cara M. Robertus, Darianna Colina, Connor Monticello, Thomas Connor Donahue, Lauren Hong, Sophia Vincoff, Shrey Goel, Peter Fekkes, Luis Miguel Camargo, Kieu Lam, James Heyes, David A. Putnam, Christopher A. Alabi, Pranam Chatterjee, Matthew P. DeLisa

  267. bioRxiv (Cold Spring Harbor Laboratory)

    The first OpenBind release: An open experimental structure–affinity dataset and benchmark for structure-based AI

    Jochem Nelen, Omeir Khan, E. Charles Adams, Jasmin Cara Aschenbrenner, Warren Athol Thompson, Ali Ebrahim, Eda Çapkın, Cédric Vallée, OpenBind, Elizabeth J. Shotton, Ed Griffen, John D. Chodera, Charlotte Mary Deane, F. von Delft, Mohammed AlQuraishi, Fergus Imrie

  268. Nature Communications

    A programmable lipid-triggered allosteric site modulates LC3 LIR receptor binding activity

    Deepanshi Gahlot, Jesu Castin E, S C Mathur, Debajyoti Das, Ajit Kumar, Akanksha Arun, Chandrima Gain, Mridul Sharma, Ravi Kant Pal, Niyati Jain, Bichitra Kumar Biswal, Rajat Singh, Lipi Thukral

    Discovered via OpenAlex

  269. arXiv (Cornell University)

    FoldKit: A Python library for efficient storage and retrieval of co-folding predictions

    Jon Levine, Melissa Pathil, Samuel Nitz, Olga Lyudovyk, Benjamin D. Greenbaum

    Discovered via OpenAlex

  270. mAbs

    DyAb: sequence-based antibody design and property prediction in a low-data regime

    Joshua Yao-Yu Lin, Jennifer L. Hofmann, Andrew Leaver‐Fay, Wei‐Ching Liang, Stefania Vasilaki, Edith Lee, Pedro O. Pinheiro, Nataša Tagasovska, James R. Kiefer, Yan Ping Wu, Franziska Seeger, Richard Bonneau, Vladimir Gligorijević, Andrew M. Watkins, Kyunghyun Cho, Nathan C. Frey

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 2. Model-based design · 2.4 LLM-based

  271. Journal of Translational Medicine

    RFdiffusion-designed CLDN18.2 T-cell engager coupled with dendritic-cell supplementation enhances antitumor immunity in gastric cancer

    Haoxuan Kan, Guoyang Niu, Zihan Wan, Yifan Zou, Jihuan Wang, Yihan Xu, Haojun Yang, Zekuan Xu, Bowen Li

    Discovered via OpenAlex

  272. bioRxiv (Cold Spring Harbor Laboratory)

    PMPNN-DDG: an accurate machine learning-based ΔΔ G prediction pipeline trained on a novel interpretable feature set extracted from ProteinMPNN

    Sajid Ahmed, Md Rafsan Jani

    Discovered via OpenAlex

  273. bioRxiv (Cold Spring Harbor Laboratory)

    WaterFlow: Prediction of Ordered Water Molecule Positions on Protein Structures

    Vratin Srivastava, Huanghao Mai, Marcus D. Collins, James M. Holton, Michael E. Wall, Stephanie A. M. Wankowicz

    Discovered via OpenAlex

  274. PLoS ONE

    Assessment of generative de novo peptide design methods for G protein-coupled receptors

    Hannes Junker, Clara T. Schoeder

    Discovered via OpenAlex

  275. Bulletin of Faculty of Pharmacy Cairo University 

    Formulation Strategies for Next-Generation Bispecific Antibodies: Design Considerations and Stability Implications

    Priya Patel, Vaibhav Bhatt, Nirav Patel

    Discovered via OpenAlex

  276. ACS Chemical Biology

    Enhancing De Novo Designed Peptides and Proteins via Irreversible Covalent Isoquinolinium Capture

    Paul M. Levine, Patrick W. Erickson, Timothy W. Craven, Aaron T. Balana, Derrick R. Hicks, Green Ahn, Chan J. Kim, Lisa S. Brandenburg, Wei Yang, Danielle P. Johnson Erickson, David A. Baker

  277. bioRxiv (Cold Spring Harbor Laboratory)

    A Mammalian High-Throughput Screen for AI-Designed Peptide-Guided Protein Degraders

    Lin Zhao, Anuoluwapo A Mattix, Aastha Pal, Tong Chen, Sophia Vincoff, Lauren Hong, Diana Renteria, Sunetra Sase, Adeline L. Vanderver, Daniel Matson, Pranam Chatterjee

  278. bioRxiv (Cold Spring Harbor Laboratory)

    Programmable De Novo Design of Mesoporous Protein Crystal Frameworks

    Zhe Li, Shunzhi Wang, William Sheffler, Yang Hsia, Byeongdu Lee, Greg L. Hura, Muammer Y. Yaman, Bo Liu, Ryan D. Kibler, Neville P. Bethel, David Chmielewski, Danny D. Sahtoe, Wei Yang, Hao Shen, Hanlun Jiang, Una Nattermann, Yunbing Shui, Haoheng Liu, Hannah Nguyen, Alex Kang, Justin A. Decarreau, Andrew J. Borst, Asim K. Bera, Banumathi Sankaran, David S. Ginger, David A. Baker

  279. JACS Au

    Enhanced Sampling of Protein Conformations in AlphaFold3 with Repulsive Bias in the Diffusion Generative Model

    Jun Ohnuki, Kei-ichi Okazaki

    Discovered via OpenAlex

  280. Angewandte Chemie International Edition

    De Novo Design of a Protein Binder to Probe Gas Channel and Enhance the Oxygen Tolerance of [NiFe]‐Hydrogenase

    Xuan Sun, Qi xiao, Nan Zhang, Wenjin Li, Hang Luo, Yanxin Gao, Leyan Zhang, Yilin Fan, Peiyu Jiang, Yucen Huang, Geng Wu, Liyun Zhang

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.3 RoseTTAFold-based

  281. Zenodo (CERN European Organization for Nuclear Research)

    SPICE: Physics-supervised reinforcement learning for environment-adaptive protein design

    Jingwen Kuang

    Discovered via OpenAlex

  282. FEBS Letters

    Engineering peptides into antibodies—opportunities and strategies for therapeutic innovation

    Jinling Wang, Ruslana Romaniuk, Hristo L. Svilenov

    Discovered via OpenAlex

  283. Zenodo (CERN European Organization for Nuclear Research)

    Data for: Programmable De Novo Design of Mesoporous Protein Crystal Frameworks

    Zhe Li, David A. Baker

  284. International Journal of Molecular Sciences

    Special Issue “New Insights into Bioactive Peptides: Design, Synthesis, Structure–Activity Relationship (2nd Edition)”

    Flavia Anna Mercurio, Marilisa Leone

    Discovered via OpenAlex

  285. Journal of Cheminformatics

    Research EnzyPred: a general model for predicting enzyme–substrate interactions using deep learning, parallel LoRA, and, natural language processing-inspired approaches

    Luis Fernando Salas Nuñez, Alvaro A. Barrera-Ocampo, Paola A. Caicedo, Natalie Cortés, Edison H. Osorio, Óscar Alberto Álvarez Solano, María Francisca Villegas-Torres, Andrés Fernando González Barrios

    Discovered via OpenAlex

  286. International Journal of Scientific Engineering and Research

    AI-Driven Enzyme Engineering: A Data-Efficient Framework for Designing Next-Generation Biocatalysts

    Utkarsh Agrawal

    Discovered via OpenAlex

  287. Journal of Nanobiotechnology

    Recent advances in fabrication strategies, functional modulation and healthcare applications of native protein-based hydrogels

    Fuwei Sun, Qiyang Qu, Mingyang Sun, Tuo Zhang, Jiachen Zang, Chenyan Lv, Guanghua Zhao, Zhongjiang Wang

    Discovered via OpenAlex

  288. UNC Libraries

    Engineering Dual Peptide-Decorated Extracellular Vesicles to Enhance Retention and Functional Recovery After Myocardial Infarction

    Rayhan Shahid Shanavas

    Discovered via OpenAlex

  289. Biotechnology Advances

    Engineering and design of artificial enzymes for non-natural biocatalysis in whole cells

    Hanchen Zhao, Qiqi Liu, Juan Guo, Shuangxi Gu

    Discovered via OpenAlex

  290. Alzheimer s Research & Therapy

    A third-generation, high-affinity biparatopic anti-tau antibody inhibits intracellular tau aggregation seeded by Alzheimer’s brain extracts

    Eric Hatterer, Lucile Broyer, Sara Pecoraro, Fabien Cusin, Naz Simsek, John J. P. Brevé, Mathieu Clavel, Kevin Llewelyn Batenburg, Bart Klein, Thuur Zuidweg, Kristin Piché, Jérémie Bourguignon, Margot Bonnet-Gamard, Pauline Malinge, Franck Gueneau, Valéry Moine, Nadia Anceriz, Krzysztof Masternak, Nicolas Fischer, Torleif Tollefsrud Gjølberg, Jenny Skjermo Telstad, Gaia Calamera, Simone Mester, Wiep Scheper, Wilma D. J. van de Berg, Jean‐Philippe Courade

    Discovered via OpenAlex

  291. arXiv (Cornell University)

    Natural-Language-Guided Generator-Agnostic Shortlisting for Protein Binder Design

    Gyubok Lee, Kiwoong Yoo, Jimin Seo, Jiyoun Kim, Kyunghoon Hur, Edward Choi

    Discovered via OpenAlex

  292. Nature Synthesis

    Access to all stereoisomers of chiral alcohols with multiple stereocentres enabled by machine learning-empowered protein engineering

    Zhenyu Lu, Jiahui Zhou, Tao Han, Zhaoyuan Zhang, Weihua Xu, Yixin Cen, Cheng Jiang, Jingxin Zhang, Yue Guo, Chunyang Cao, Meilan Huang, Qi Wu

    Discovered via OpenAlex

  293. Signal Transduction and Targeted Therapy

    Accelerating protein engineering: an integrated framework combines protein language models and epistatic landscape modeling

    Jeongyoung Koo, Young‐Ho Park, Sun‐Uk Kim

    Discovered via OpenAlex

  294. bioRxiv (Cold Spring Harbor Laboratory)

    From Code to Cure: Computationally Designed BMP-2 Binders Using AI-Integrated Pipelines for Controlled Bone Regeneration

    Ben Burress, Arash Asgari, Jonathan Dorogin, Karly M. Fear, Cassandra Gonzalez, Justin E. Svendsen, Dylan Merrill, Marian H. Hettiaratchi, Parisa Hosseinzadeh

    Discovered via OpenAlex

  295. Nature Communications

    Accelerating protein design by scaling experimental characterization

    Jason Qian, Lukas F. Milles, Basile I. M. Wicky, Robert J. Ragotte, Amir Motmaen, Andrew J. Borst, Rebecca Skotheim, Sebastian Ols, Brian Coventry, Xinting Li, Ryan D. Kibler, Inna Goreshnik, Marc Expòsit, Karin Loré, Lance J. Stewart, David A. Baker

    Curated by Papers for Protein Design Using Deep Learning · 4.5 GNN-based · 4.Scaffold to Sequence

  296. Nature Communications

    AI-enabled discovery and biochemical optimization of minibinders targeting cancer cell-surface proteins

    Bianca Broske, Benjamin A. McEnroe, Sophie C. Binder, Tim Noah Kempchen, Caroline I. Fandrey, Elisabeth Tan, Dominic Ferber, Michelle C.R. Yong, Marie Kleinert, Julia M. Messmer, Peter Konopka, Alexander Hoch, Katja Blumenstock, Jan M. P. Tödtmann, Johannes Oldenburg, Heiko Rühl, Alexander Semaan, Prof. Marieta I. Toma, Kristina Markova, Sebastian Kobold, Tim Rollenske, Matthias Geyer, Stephan Menzel, Tobias Bald, Jonathan Leo Schmid-Burgk, Gregor Hagelueken, Michael Hölzel

    Discovered via OpenAlex

  297. Weizmann Institute of Science Institutional Repository

    Towards high-throughput protein design.

    Jonathan (Biochemistry) Weinstein

    Discovered via OpenAlex

  298. International Journal of Computer Applications

    AI-Powered Drug Discovery A Framework for Accelerating Peptide Therapeutics Development

    Ramesh Kumar Ramu

    Discovered via OpenAlex

  299. PLoS Computational Biology

    CLDN18.2 antibody design with protein language models: A deep learning optimization framework

    Tao Qu, Lingyan Yuan, Weiran Cui, Jiatian Tang, Zhitong Bing, Xianghong Xu, Jizheng Duan, Qiong Yang, Hui Cai

    Discovered via OpenAlex

  300. Journal of Medicinal Chemistry

    HighMorph: De Novo Cyclic Peptide Sequence Design via Protein–Protein Interaction Recapitulation

    Minhui Lan, Chengyun Zhang, Wentong Wang, Hu Haomeng, Huitian Lin, Sen Cao, Jingjing Guo, Hongliang Duan

    Discovered via OpenAlex

  301. arXiv (Cornell University)

    FAR-DPO: Feasibility-Aware and Robust Direct Preference Optimization for Cyclic Peptide Design

    Guofeng Zhang, Rong Han, Xiaoyu Wang, Zhiyun Li, Zongbo Han, Xiaohong Liu, Guangyu Wang

    Discovered via OpenAlex

  302. Journal of Chemical Information and Modeling

    To ML-Predict or Not to ML-Predict: The Impact of Machine Learning-Predicted Protein Structures on FEP Accuracy and Data Augmentation

    Parker Dryja, Morné Muller, Monique Horn, Ilya A. Balabin, Zackery W. Dentmon, Prawin Rimal, Yuri Karl Peterson, Fourie Joubert, Thomas M. Kaiser, Pieter B. Burger

    Discovered via OpenAlex

  303. Trends in Food Science & Technology

    Mechanism-guided engineering of food-derived anti-fatigue peptides from molecular design to protease-constrained production

    Xiaoyu Ma, Ximing Yang, Xinran Liu, Wenshuo Zhao, Ling Zhang, Shuzhen Cheng, Ming Du

    Discovered via OpenAlex

  304. bioRxiv (Cold Spring Harbor Laboratory)

    β-lactoglobulin a new whey: Computational redesign improves stability and nutritional composition

    Maija Greis, Ulysse Castet, Elsa Berlin, Sofia Klangby, Oliwia Bancerz-Aleksiejczuk, Francisco Vilaplana, Julia Katharina Keppler, Elton Paul Hudson

    Discovered via OpenAlex

  305. arXiv (Cornell University)

    Leveraging generative hallucination and biophysics-informed modeling for unified biomolecular sequence-structure co-design

    Xuefeng Liu, Mingxuan Cao, Xiao Luo, Songhao Jiang, Tobin R. Sosnick, Jinbo Xu, Louis Maher, Rick Stevens

    Discovered via OpenAlex

  306. arXiv (Cornell University)

    Protein Structure Prediction: From Evolutionary Constraints to Generative Modeling

    Wengan He, Yongsheng Luo, Lihong Jiang, Wenhui Xu, Yu Li

    Discovered via OpenAlex

  307. Journal of Medicinal Chemistry

    Structure-Based Design of First Ndc80 Loop-Targeting Peptide Disrupting Ndc80–Nuf2 Interaction for Hepatocellular Carcinoma Therapy

    Xing Jin, Miaomiao Niu, Yifei Geng, Liqiao Han, Yuting Wang, Xianzhang Huang, Qiaoxuan Zhang

    Discovered via OpenAlex

  308. Journal of the American Chemical Society

    Sequence-Directed Hierarchy of Supramolecular Peptide Bilayers and Heme Cofactor Insertion

    Jesse L. Prelesnik, Andrew Lau, Nathan C. Laud, Kelsie J. Li, Yuzi Liu, Henry Chan, Harry Christopher Fry

    Discovered via OpenAlex

  309. FEBS Journal

    Structure‐ and deep learning–guided engineering of a size‐minimized CRISPR /Cas

    Smith Le, Trung Thanh Thach

    Discovered via OpenAlex

  310. arXiv (Cornell University)

    Large Discovery Models: Empirically-grounded Model-Based Open-Ended Search

    Zhongwei Yu, Yan Song, Xue Yan, Anjie Liu, Xingyu Lu, Yihang Chen, Huichi Zhou, Siyuan Guo, Luoyang Sun, Sihan Chen, Xiangning Yu, Jun Wang

    Discovered via OpenAlex

  311. bioRxiv (Cold Spring Harbor Laboratory)

    De novo design of autocatalytically forming intra- and intermolecular isopeptide bonds to construct rigid covalent protein assemblies

    Lukas F. Milles, Timothy F. Huddy, ANN CARR, Yang Hsia, Xinting Li, Alex Kang, Banumathi Sankaran, Asim K. Bera, David A. Baker

  312. The EMBO Journal

    FAF1 and FAF2 enhance unfolding by p97-UFD1-NPL4 complex enabling rational design of p97 activators

    Pritha Dasgupta, Ian R. Kelsall, Gaurav Anand, Anna Pérez‐Ràfols, Thomas A. Jowitt, Axel Knebel, Robert Gourlay, Glenn Robert Masson, Yogesh Kulathu

    Discovered via OpenAlex

  313. arXiv (Cornell University)

    Valhalla: A Layered Knowledge-State and Service-Governance Framework for Long-Term Scientific Knowledge Work

    Yuyang Zheng, Nan Li, Wenxia Deng, Li Yan, Xiang Li, Si Chen

    Discovered via OpenAlex

  314. Iconic Research and Engineering Journals

    A Computational Framework for Erythropoietin Protein Synthesis and Optimization: Integrating Protein Language Models, AlphaFold3 Structural Prediction, and Bayesian Optimization

    Gaurav Nandagawli

    Discovered via OpenAlex

  315. Bioinformatics

    Bridging linguistic reasoning and biophysical reality toward peptide engineering via instruction-tuned language modeling

    Yang Kaijun, Tianxiang Wu, Wenbo Zhang, Pengyong Li

    Discovered via OpenAlex

  316. bioRxiv (Cold Spring Harbor Laboratory)

    Protein design to broadly reprogram engineered T cell function

    Scott E. Boyken, Sean Merillat, Robert A. Langan, Howell F. Moffett, Brian Coventry, Françoise Haeseleer, Kevin G. Haworth, Inna Goreshnik, Joseph DeSautelle, John Chukinas, Bradley Hammerson, Thaddeus M. Davenport, Duy Nguyen, Rupesh H. Amin, Shujun Yuan, G. Wink, Brian D. Weitzner, Aaron Edward Foster, David A. Baker, Marc J. Lajoie

  317. Molecular Biology and Evolution

    Redesign of energetically frustrated regions rescues function in defective T4 clamp loaders

    Siddharth Nimkar, Thu Nguyen, Deepti Karandur, Subu K. Subramanian, Mike E. O’Donnell, John Kuriyan

    Discovered via OpenAlex

  318. Advanced Science

    Computationally Evidence‐Grounded Sequence‐First Design of Peptide Binders

    Wenze Ding

    Discovered via OpenAlex

  319. Journal of Translational Medicine

    IgY as a versatile antibody platform for precision diagnostics and targeted biotherapeutics: a review

    Shi-Ying Lai, Jing Lei, Si-Yi Zeng, Ruo-Xi Wang, Zhi-Tong Li, Tayier Keremu, Lan Chen, Jiang Pi, Huan-Shao Huang, Yan-Guang Cong, Jun‐Fa Xu

    Discovered via OpenAlex

  320. Journal of Cheminformatics

    MMAllo: a multimodal deep learning framework and GaMD simulations for predicting protein allosteric sites and allosteric mutations

    Pengyin Zhang, Yi He, Hanwen Liu, Rui Lai, Weiwei Han

    Discovered via OpenAlex

  321. npj Drug Discovery.

    On the generalization and usability of cofolding models for GPCR drug discovery

    Lichirui Zhang, Richard A. Friesner, Edward B. Miller, João Rodrigues

    Discovered via OpenAlex

  322. Molecules

    Beyond Branching: Unlocking the Catalytic Versatility of Branching Enzymes for the Design of Diverse α-Glucan Structures

    Maurice K.H. Essers, Hans Leemhuis, Johannes Hendrik Bitter, L.A.M. van den Broek

    Discovered via OpenAlex

  323. MedScien

    Tau Protein Pathology and Tau-Targeted Therapeutic Strategies in Alzheimer’s Disease: Mechanisms, Clinical Evidence and Future Perspectives

    Zhuoyu Wang

    Discovered via OpenAlex

  324. Advanced Healthcare Materials

    MAP Crosslinker Chirality Regulates Macrophage Polarization Through MD‐2 Engagement and Enables Tunable Immunomodulation Through Novel Peptide Design

    Alejandra Suarez‐Arnedo, Jeremy L. Thomas, Yining Liu, Pablo Cordero Alvarado, Amy Kim, Maria April Chavez Espinoza, Leica Harvey, Koravit Poysungnoen, Fayanne Lin, Zhiyou Ye, Tatiana Segura

    Discovered via OpenAlex

  325. Journal of Chemical Information and Modeling

    Machine-Learning-Guided Design of Antifreezing Peptides

    Md Nazmul Islam Shuzan, Jialun Wei, Jie Zheng

    Discovered via OpenAlex

  326. Frontiers in Bioinformatics

    Single cell mapping of B and T cell dynamics in breast cancer lymph node metastasis

    Sajid Khan, Sabahat Jamil, Muhammad Hamza, Zarlish Attique, Suping Zhang

    Discovered via OpenAlex

  327. Nature Communications

    IL-2 mutein-engrafted antibody MHS552 selectively expands functional regulatory T cells in nonclinical models and healthy participants

    Igor Radanović, Michael DiDonato, Anouk C. Meijs, David A. Schubert, Yaiza Diaz De Durana, Andrea Kießling, Thierry Flandre, Hannah Morgan, Claudia Simonett, Justin McMullen, Manon A. A. Jansen, Thomas P. Buters, Mahdi Saghari, Pim Gal, Jacobus J. Bosch, Sjoerd H. van der Burg, Susanne Osanto, Morten Aavad Bagger, Claudio Calonder, Darbi Witmer, Ülrike Sommer, Frank Waldron-Lynch, Peter Gergely, Nadège Pelletier, Nicole Hartmann, Esther Kamphausen, Magdalena Kistowska, Helene Marsot, A Auger-Sarrazin, Céline Rauld, Camille Regairaz, Timothy I. M. Tree, Yann D. Ladner, Naomi B. Klarenbeek, Matthijs Moerland, Robert Rißmann, Glen Spraggon, Leona Gabryšová

    Discovered via OpenAlex

  328. arXiv (Cornell University)

    How to Spend Your Oracle Budget: Practical Guidance for Protein Structure Prediction Models

    Aleksandra Kalisz, Jack Simons, Krisztina Sinkovics, Noam Ghenassia, Shikha Surana, Henry Moss, Paul Duckworth

    Discovered via OpenAlex

  329. bioRxiv (Cold Spring Harbor Laboratory)

    NDST1 as a substrate-reduction target in Mucopolysaccharidosis type IIIC: virtual screening, microsecond molecular dynamics, and peptide design

    Keshav Mohan, Yash Bhargava

    Discovered via OpenAlex

  330. Zenodo (CERN European Organization for Nuclear Research)

    [Re] Robust deep learning–based protein sequence design using ProteinMPNN

    Huang, Christopher, Ryan Ahn, Wenhao Lu

    Discovered via OpenAlex

  331. ACS Synthetic Biology

    An Artificial Intelligence Model for Translating Natural Language into Functional De Novo Proteins

    Timothy P. Riley, Mohammad S. Parsa, Pourya Kalantari, Ismail Naderi, Kiana Azimian, Nemya Begloo, Oleg S. Matusovsky, Eliot Osher, Devika Prabhakaran, Rahul Yadav, Klem Simelis, Indran Mathavan, Jeeven Singh, Kooshiar Azimian, Kathy Y. Wei

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 5.4 Transformer-based · 5.Function to Sequence

  332. FEBS Letters

    The sweet spot in protein design—Where deep learning meets first principles

    Gabriel Cia, Gabriele Orlando, Damiano Cianferoni, Rob van der Kant, Javier Delgado, Erik Verschueren, Frédéric Rousseau, Luis G. Serrano, Joost W. H. Schymkowitz

    Discovered via OpenAlex

  333. Cell Death Discovery

    Targeting the ERO1A–PDIA1 redox axis in triple-negative breast cancer with AI-designed minibinders

    Alice Marrazza, Sara Baroni, Ersilia Varone, Alessandro Cherubini, Serena Germani, Giorgia Maria Renna, Daniele Generali, Manuela Milani, Mirko Marabese, Monica Favagrossa, Alessia Porta, Giorgia Giordano, Alfredo Cagnotto, Luca Guarrera, Marco Gobbi, Bo-Ram Jin, Jaehyung Cho, Marten Beeg, Ester Zito

    Discovered via OpenAlex

  334. Journal of Medicinal Chemistry

    PepGate: A Dual-Path Diffusion Framework for ACE Inhibitory Peptide De Novo Design

    Wanhao Sun, Xihe Yang, Xin Huang, Neng Xiong, Hongru Feng, Yuanjiang Pan

    Discovered via OpenAlex

  335. Intentional Fibonacci-Lucas-guided peptide design as a prospective experimental factor: A falsifiable, patient-centred framework for GLP-1, GIP and related therapeutics within the Geier equilibrium programme (A first approach)

    Stefan A Geier, Caroline Geier, Stephanie Geier, Constantin Geier, Katharina Geier, Nora Blättermann-Goldstein, Michèle Geier-Noehl

    Discovered via OpenAlex

  336. Journal of Chemical Theory and Computation

    Prediction of Distal Mutation Effects in Enzymes via Integration of Molecular Dynamics Descriptors and Zero-Shot Model

    Yiqiu Wang, Ding Luo, Shuming Cheng, Binju Wang

    Discovered via OpenAlex

  337. Cell Death Discovery

    Calreticulin-targeting L-asparaginase-flagellin conjugate enhances Salmonella-mediated antitumor efficacy

    Dinh-Huy Nguyen, Aqeel Rana Afzal, Phuong Thi-Minh Nguyen, Quoc-Thai Do-Ba, Khuynh Van Nguyen, Wan-Sik Lee, Jung-Joon Min, Yeongjin Hong

    Discovered via OpenAlex

  338. Results in Chemistry

    Plastic-degrading enzymes: Advances, challenges, and industrial prospects in enzyme engineering and computational design

    Vivek B. Pattani, Jinesh P. Kaneriya, Krishna Joshi, Gaurav V. Sanghvi

    Discovered via OpenAlex

  339. Journal of Agricultural and Food Chemistry

    Enzyme Engineering: From Classical Strategies to AI-Driven Biocatalyst Design

    Mati Ullah, Muhammad Rizwan, Vivian Andoh, Ali Raza, Muhammad Naeem, Muhammad Ihtesham Waheed, Yong Chen

    Discovered via OpenAlex

  340. bioRxiv (Cold Spring Harbor Laboratory)

    Safety first: input screening for protein design tools

    Phil Palmer, Nicole A. Teran, Nicole E. Wheeler, Jaime M. Yassif

    Discovered via OpenAlex

  341. bioRxiv (Cold Spring Harbor Laboratory)

    De novo design of a protein fold for small-molecule binding through aromatic π stacking

    Stephanie T. Ouchida, Maggie Horst, Xuxu Gou, Ian J. Bakanas, A. Katherine Hatstat, Lee Schnaider, Morgan E. Diolaiti, Alan Ashworth, William F. DeGrado

    Discovered via OpenAlex

  342. bioRxiv (Cold Spring Harbor Laboratory)

    Coevolution-informed Bayesian optimization for sample-efficient protein design

    Dulitha Prasanna Kulathunga, Divyanshu Shukla, Davit A. Potoyan

    Discovered via OpenAlex

  343. Advanced Science

    AI Designed Conformation Locking Peptides Target STING to Restore Diabetic Wound Healing

    Ru‐hong Zhang, Haojie Fu, Zhe Wang, Xuanzhou Chen, Ruhong Zhang, Xudong Wang, Dong Zhang, Xiang Li, Datao Li

    Discovered via OpenAlex

  344. Journal of Asian Medical Students Association

    Drug Repurposing and De Novo Novel Monoclonal Antibody Design for Chikungunya Virus: A Two-pronged Bioinformatics Analysis

    Rosalyn Yuen Yim Tang, Man Yi Kristen Lo, Matthew Yeung, Hui Guan Ho, Wing Tung Chou, Enoch Chu

    Discovered via OpenAlex

  345. Archives of Microbiology

    Microbial lipases: advances in metagenomics and artificial intelligence for enzyme discovery and engineering

    Km. Priti, Harish Chandra, Kalpana Sagar

    Discovered via OpenAlex

  346. Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics

    Local energetic frustration: Protein evolution, conformational dynamics and design in the age of AI

    Franco L. Simonetti, Eli J. Draizen, Rocío Espada, R. Gonzalo Parra

    Discovered via OpenAlex

  347. ChemRxiv

    Co-folding models localize enzyme active sites but fail to accurately predict enzyme–substrate complex structures

    Daniil Lepikhov, Ariane Nunes‐Alves

    Discovered via OpenAlex

  348. Protein Science

    Soluble protein analog selection engine (SPASE) : An automated AI ‐powered server to improve protein engineering workflows

    Sacha Thierry Larda, Alex Paré, Nicolas Doucet

    Discovered via OpenAlex

  349. Chemistry - A European Journal

    Fibrilpaint: A Class of Amyloid‐Targeting Peptides

    Júlia Aragonès Pedrola, Françoise A. Dekker, Katrin Guttmann, Litske M. van Leeuwen, Shalini Singh, Guy Mayer, Tommaso Garfagnini, Assaf Friedler, Stefan Rüdiger

    Discovered via OpenAlex

  350. Microbiology Spectrum

    Allosteric effects of CDR-H3 mutations modulate binding and neutralization of a conserved SARS-CoV-2 RBD-targeting antibody

    Muhammad Waqas Nasir, QIyun Liang, Jun He, Umer Rashid, Jiabing Wu, Yong Gao

    Discovered via OpenAlex

  351. npj Digital Medicine

    Computational design of multi-objective optimized peptide disrupting Tim-3 galectin9 checkpoint

    Huihui Yan, Jiayi Chen, Weijia Yang, Yiwen Zhang, Buyong Ma, Ping Huang, Minghua Ge

    Discovered via OpenAlex

  352. bioRxiv (Cold Spring Harbor Laboratory)

    Dual-Specific Antibody Design Using Artificial Intelligence

    Michael Peer, Inbar Amit, Yael Diesendruck, Ziv Erlich, Yonit Ben David, Meital Gadrich, Nino Oren, Tzvika Hartman, Sharon Fischman, Guy Nimrod, Marek Štrajbl, Avi Haleva, Reshef Shilon, Yehezkel Sasson, Reut Barak-Fuchs, Itzhak Meir, Liron Danielpur, Yuval Mor-Scheerer, Nitzan Dubovski, Tal Vana, Dagan Hadar, Anna Voropaev, Yair Fastman, Yanay Ofran

    Discovered via OpenAlex

  353. bioRxiv (Cold Spring Harbor Laboratory)

    De novo design of small-molecule–induced conformational change

    Jeffrey Chang, Nicholas F. Polizzi

  354. Chemical Engineering Journal

    AI-driven de novo protein design coupled with high-throughput screening: Challenges and opportunities

    Ruei-En Hu, I‐Son Ng

    Discovered via OpenAlex

  355. bioRxiv (Cold Spring Harbor Laboratory)

    Blending physics-based and inverse folding models to disentangle variant effects on stability and function

    Ezequiel Alejandro Galpern, Xavier Soler Sanchis, Charles W. J. Pugh, Federico Billeci, Jonathan Frazer, Mafalda Dias

    Discovered via OpenAlex

  356. Journal of Peptide Science

    Peptide Therapeutics for Solid Tumors: Functional Classes, AI‐Enhanced Discovery and Clinical Advances

    Jinqiu Liang, Xiaochuan Tang, Haoqi Li, Yan Fang, Feng Jiang

    Discovered via OpenAlex

  357. bioRxiv (Cold Spring Harbor Laboratory)

    HaloMPNN: retraining ProteinMPNN on halophilic proteomes for salt-tolerant enzyme design

    Alyssa Lu Lee, Austin Seamann, Gwendolyn Chung, Clairie Zhao, Rohan Maddamsetti, Sagar D. Khare

    Discovered via OpenAlex

  358. bioRxiv (Cold Spring Harbor Laboratory)

    Seed-Guided De Novo Design Expands the Structural Diversity of Antitoxin Protein Binders

    Dustin Britton, Dia A. Ghose, Jackson C. Halpin, Foster Birnbaum, Kruthi Gundu, Shaunak Raval, Malvina Papanastasiou, Steven A. Carr, Amy E. Keating

    Discovered via OpenAlex

  359. Research Square

    Integrated Machine Learning, Molecular Docking, and Molecular Dynamics Simulations Design Novel Peptide Inhibitors of Rabies Virus Glycoprotein

    Harshada Sawant, Ashish Asrondkar, Vrushali Patil

    Discovered via OpenAlex

  360. ACS Applied Bio Materials

    Peptide-Functionalized Gold Nanoparticles Targeting PD-L1: Design via a Molecular Dynamic Driven Approach and Further Experimental Validation

    Micaela Giannetti, Marina Gobbo, Lucio Litti, Isabella Caligiuri, Flavio Rizzolio, Moreno Meneghetti, Claudia Mazzuca, Antonio Palleschi

    Discovered via OpenAlex

  361. Colloids and Surfaces B Biointerfaces

    Biomimetic engineering of a fortified ice composite with enhanced mechanical properties

    Chen Adar, Yulia BARON, Baruch Rofman, Maya Bar Dolev, Liat Bahari, Victor Yashunsky, Vera Sirotinskaya, Oded Shoseyov, Ido Braslavsky

    Discovered via OpenAlex

  362. bioRxiv (Cold Spring Harbor Laboratory)

    Intra-Protein Interfaces Control Folding Dynamics and Mechanical Stability in a De Novo Designed Repeat Protein

    Mélanie Weiss, Anna Lisa Heit, Lukas F. Milles, Johannes Stigler

    Discovered via OpenAlex

  363. Results in Chemistry

    HMRLBA: A hierarchical multi-scale representation learning model for predicting protein-ligand binding affinity

    Zhiwei Ji, Zhongyu Xu, Kai Chen, Junchi Yang, Zhijin Li, Jinhu Huang

    Discovered via OpenAlex

  364. Bioinformatics

    Synthetic sequence alignments as programmable probes of learned conformational landscapes in deep learning protein structure predictors

    Jannik Adrian Gut, Noah Kleinschmidt, Thomas Lemmin

    Discovered via OpenAlex

  365. Chinese Science Bulletin (Chinese Version)

    Advances in de novo protein design for anti-infective applications

    Jie Yin, 顾子春, Yuchen Sun, Liang Tao

    Discovered via OpenAlex

  366. Nature Communications

    High-throughput engineering of bispecific antibodies to enhance macrophage-mediated cytotoxicity of B-cell lymphoma

    Carlota Pagès, Juliano Ribeiro, Thomas N Wienclaw, Anna Meglan, Lauren M. Sloat, Matheus Silva, Jasmine Blandin, José Velarde, Kyle Vaccaro, Carolin Sebastiany, Patricia Fernández-Guzmán, Cynthia K. Hahn, Marta Crespo, Kipp Weiskopf

    Discovered via OpenAlex

  367. bioRxiv (Cold Spring Harbor Laboratory)

    Optimized Multiple Circular Sequence Alignment for Cyclic Peptide Motif Discovery

    Ye Yuan, Zhe Li, Kaiqiang Hu, Pengwei Pan, Fang He

    Discovered via OpenAlex

  368. Journal of Pharmaceutical Analysis

    Artificial Intelligence-Driven De Novo Peptide Drug Design: Architectures, Pipelines, and Translational Challenges

    Zixiao Wang, Lili Sun, Yao Li, Fang Yang, Yu Chang

    Discovered via OpenAlex

  369. Plant Communications

    A computational framework integrating a protein language model with alchemical simulation for gain-of-function enzyme design

    Long‐Can Mei, Jian Wu, Lijun Chen, Yan-Mei Ni, Xiaoting Wang, Fan Wang, Hong‐Yan Lin, Guang‐Fu Yang

    Discovered via OpenAlex

  370. bioRxiv (Cold Spring Harbor Laboratory)

    A modular platform for scalable recombinant production of highly toxic bacterial proteins

    Rina Fraenkel, Inbar Cahana, Tomer Sivan, Tal Fisher, Hen Nadav, shani bruchim, Noam Deouell, Shani Cheskis, Maor Shalom, Lionel Imbert, Asaf Levy, Netanel Tzarum

    Discovered via OpenAlex

  371. Advanced Science

    A Generative Neuro‐Symbolic AI for Protein Sequence Design

    Marianne Defresne, Delphine Dessaux, Samuel Buchet, Lucie Barthe, Liza Ammar Khodja, Bessam Azizi, Valentin Durante, Gianluca Cioci, Simon de Givry, Alain Roussel, Luis Fernando Garcia-Alles, Thomas Schiex, Sophie Barbe

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 4.1 MLP-based · 4.Scaffold to Sequence

  372. bioRxiv (Cold Spring Harbor Laboratory)

    Beyond Generic Signal Peptides: ApexSP Enables Cargo-Specific Secretion Design

    Chunyi Yang, Ruiyang Hou, Zhenyu Ma, QiuYan Kang, Shuojing Zuo, Limei Xu, Min Xiao, Xiuyun Wu, Xukai Jiang

    Discovered via OpenAlex

  373. Nature

    Miniaturizing and modifying natural proteins with Raygun

    Kapil Devkota, Daichi Shonai, Yiwei Mao, Young Su Ko, Wei Wang, Scott H. Soderling, Rohit Singh

    Discovered via OpenAlex

  374. Current Opinion in Chemical Biology

    Generative artificial intelligence for enzyme design and biocatalysis

    Lasse Middendorf, Noelia Ferruz

    Discovered via OpenAlex

  375. bioRxiv (Cold Spring Harbor Laboratory)

    Prebiotic cationic amino acids support formation of an ancient protein fold

    Sota Yagi, Aditya Kumar Padhi, Khushboo Bhagat, Kam Y. J. Zhang, Shunsuke Tagami

    Discovered via OpenAlex

  376. Zenodo (CERN European Organization for Nuclear Research)

    Integrating protein language model with alchemical simulation for gain-of-function enzyme design

    Long-Can

    Discovered via OpenAlex

  377. Frontiers in Bioengineering and Biotechnology

    Recent advances in multimodal foundation model-enabled peptide screening and optimization for smart biomaterials and functional tissue engineering

    Chen Ding, Yuxi Luo, Ximiao Yu, Yingying Lei, Wenping Zhang, Xun Wang, Jiadi Gan

    Discovered via OpenAlex

  378. Nature Biotechnology

    Property guidance for protein sequence generative models with ProteinGuide

    Junhao Xiong, Ishan Gaur, Maria Lukarska, Hunter M. Nisonoff, Luke M. Oltrogge, David F. Savage, Jennifer Listgarten

    Discovered via OpenAlex

  379. Journal of Chemical Theory and Computation

    Reliability of AI Methods in Drug Discovery: Evaluation of Boltz-2 for Structure and Binding Affinity Prediction

    Shunzhou Wan, Xibei Zhang, Xue Xiao, Peter V. Coveney

    Discovered via OpenAlex

  380. bioRxiv (Cold Spring Harbor Laboratory)

    Transplanting enzyme active site geometry into antibody CDRs for catalytic antibody design

    Yaojun Zhu

    Discovered via OpenAlex

  381. Molecular Pharmaceutics

    Integrating Tumor Targeting and Half-Life Extension into a Dual-Surfaced Single-Domain ADAPT Protein

    Emma Larsson, Moeen Ud‐din, Athanasios Bitzios, Enrique Recasens Pérez-Vera, Hanna Tegel, Anna Orlova, Толмачев Владимир Максимилианович, Anzhelika Vorobyeva, Sophia Hober

    Discovered via OpenAlex

  382. Synthetic and Systems Biotechnology

    Artificial intelligence catalyzes antimicrobial peptide design

    Yongqiang Liu, Jie Hu, Ning Zhang, Yinqi Bai, Yuan Yao, Gaoxiang Chen

    Discovered via OpenAlex

  383. The Journal of Immunology

    A biologically informed antibody language model framework to simulate somatic hypermutation and guide native-like antibody design 2309391

    Karenna Ng, Benjamin Némoz, Briney Bryan

    Discovered via OpenAlex

  384. The Journal of Immunology

    Experimental Validation of Variant Antibodies Guided by a Large Language Model and Optimized through Combinatorial Algorithms 2307181

    Sanaz Zebardast, Faisal Bin Ashraf, Zihao Zhang, Karen Paco, Animesh Ray, Stefano Lonardi, Ilya Tolstorukov

    Discovered via OpenAlex

  385. The Journal of Immunology

    Structural Insights and Immunogenic Enhancement of KRAS Neoantigen Recognition by TCRs in Cancer Immunotherapy 2260081

    Bassant Eldaly, Brian Baker, Smita S. Chandran, Moumita Dasgupta, Christopher Austin Klebanoff

    Discovered via OpenAlex

  386. bioRxiv (Cold Spring Harbor Laboratory)

    Sequence determinants of pathogenicity in glucose-6-phosphatase linked to glycogen storage disease type 1a

    Richard A. Stein, Emily M. Hawes, Chanel M Norphlet, Margaret H. Rakonick, Shelby A Harris, Trisha Sivam, AUDREY LUCERNE, Valentina R Da Silva, Richard M. O’Brien, Derek P. Claxton

    Discovered via OpenAlex

  387. Journal of Chemical Information and Modeling

    EnerBridge-DPO: Energy-Aware Markov Bridge Inverse Folding for Protein Sequence Design

    Dingyi Rong, Haotian Lu, Xupeng Zhang, Wenzhuo Zheng, Fan Zhang, Shuangjia Zheng, Ning Liu

    Discovered via OpenAlex

  388. Chemical Engineering Journal

    Protein-engineered Proteus myxofaciens L-amino acid deaminase synergized with magnetic nano-immobilization for efficient green synthesis of α-keto acids

    Yue Wang, Tianhua Bai, Zheng'an Yin, Xuanping Shi, Jiajia You, Minglong Shao, Xuewei Pan, Yanan Li, Zhiming Rao

    Discovered via OpenAlex

  389. Zenodo (CERN European Organization for Nuclear Research)

    BioEnzyme Designer: A Python CLI Tool for Computational Enzyme Engineering via ML-Based Catalytic Efficiency Prediction and Optimized Mutation Scoring

    Barack Ndenga, Maarouf Maman Moussa Maman

    Discovered via OpenAlex

  390. Bioinformatics

    SimBinder-IF: structure-aware antibody affinity optimization via efficient preference learning

    Xinyan Zhao, Yi-Ching Tang, Rivaaj Monsia, Victor Cantu, Ashwin Kumar Ramesh, Siyu Yang, Xiaozhong Liu, Zhiqiang An, Xiaoqian Jiang, Yejin Kim

    Discovered via OpenAlex

  391. Proteins Structure Function and Bioinformatics

    Structural and Stability Analysis of de Novo Designed Proteins Incorporating a Plant Self‐Incompatibility Motif

    Hakuto Miyoshi, Koya Sakuma, Yoshitaka Moriwaki, Naoki Aoyama, Toma Kashima, Tohru Terada, Akimasa Miyanaga, Shinya Fushinobu

    Discovered via OpenAlex

  392. Journal of Artificial Intelligence Research and Innovation

    Deep Learning and Artificial Intelligence in the Design of Angiotensin-Converting Enzyme (ACE) Inhibitory Peptides

    Zhangheng Qian, Yunuo Zhou, Ruotong Lin, Yang Hong, Yan Xu, S Li, Jiangcheng Gao, Qiurui Zhu, Heng Zheng

    Discovered via OpenAlex

  393. bioRxiv (Cold Spring Harbor Laboratory)

    Structural bioinformatics of three Epstein-Barr Virus (EBV) Integral Membrane Proteins and their water-soluble QTY analogs

    Zixuan Sun, Edward Chen, Shuguang Zhang

    Discovered via OpenAlex

  394. Journal of Microbiology and Biotechnology

    Molecular Access Engineering for Microbial Biocatalysis: from Enzyme Tunnels to Microbial Cell Factories

    Suk Min Kim

    Discovered via OpenAlex

  395. Protein Science

    De novo design of proteinaceous binders targeting the LEDGF PWWP domain

    Thibault Vantieghem, J Delepine, Sam Noppen, Steven Beelen, Matúš Drexler, Jitka Holková, Josef Houser, Václav Veverka, Dominique Schols, Sergei V. Strelkov

    Discovered via OpenAlex

  396. bioRxiv (Cold Spring Harbor Laboratory)

    AI-guided Protein Inhibitor Design for Modulating FAD-dependent Glucose Dehydrogenase Redox Output

    SuJin Lee, Eun-Ji Tak, Hyun-Jo Shim, Woo‐Chan Ahn, Kwang‐Hyun Park, Seong-Ryung Go, Haesik Yang, Eui‐Jeon Woo

    Discovered via OpenAlex

  397. Nature

    AI-redesigned starting points and outcomes enhance protein evolution

    Nicholas Andrew Krasnow, J. Y. Xu, Emily Rong Zhang, Gandhar K. Mahadeshwar, Y. Allen Tao, Julia McCreary, Colin F. Hemez, Logan E. Brown, Wei Jiang, David R. Liu

    Discovered via OpenAlex

  398. arXiv (Cornell University)

    Antigen-specific Antibody Multi-modal Foundation Model for Functional Antibody Design

    Xiaoliang Shi, Zichen Wang, Runze Ma, Zhongyue Zhang, Shuangjia Zheng

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 5.4 Transformer-based · 5.Function to Sequence

  399. Frontiers in Bioinformatics

    Analysing open-source protein folding models for nanobody binding prediction

    Yannick Vogt, Rebekka Roßberg, Jan Habermann, Pia Kluge, Wendan Xu, Mehdi Naouar, Stefan Hirschberg, Cornelius Miething, Joschka Bödecker, Maria Kalweit, Evelyn Ullrich, Gabriel Kalweit

    Discovered via OpenAlex

  400. arXiv (Cornell University)

    ABOPD: Antibody CDR Design via On-Policy Distillation

    Zhuo Yang, Jiaying He, Jiaqing Xie, Daolang Wang, Xipeng Qiu, Yuxin Wang, Tianfan Fu, Beilun Wang

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.2 Diffusion-based

  401. bioRxiv (Cold Spring Harbor Laboratory)

    De Novo Design of Protein Switches with Diffusion-Based Ensemble Sampling

    Alireza Omidi, Jiajun He, Jennifer M. Bui, Joerg Gsponer, Saifuddin Syed

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 3. Function to Scaffold · 3.4 Diffusion-based

  402. mAbs

    Glycosylation penetrance of N-X-S/T sequons in antibody variable domains: a structural survey of 19,265 human antibody structures reassessing the histidine/glutamine suppression hypothesis

    Christopher L. Gaughan

    Discovered via OpenAlex

  403. Chemical Reviews

    De Novo Design of Protein Nanopores: From Minimal Peptides to AI-Driven Design

    Anastassia Andreevna Vorobieva, Rituparna Samanta, Toon Van Thillo

    Discovered via OpenAlex

  404. Communications Materials

    Designed β-hairpin switches for controllable mechanical properties

    Gabriela Wojtan, Sofia Julin, Robert Pylkkänen, Navneet Dwivedi, Cajsa K. Malm, Anna Borisova, Timo Laakko, Marc Baldus, Piotr Batys, Pezhman Mohammadi

    Discovered via OpenAlex

  405. bioRxiv (Cold Spring Harbor Laboratory)

    ProteinSketch translates spatial intuition into protein design with bimanual interaction in VR

    Donghyeok Ma, Junyup Lee, H. C. Lee, Sang-Hyun Lee, Yeong Gyeong Oh, Ye-eun Kim, Taegyu Jin, Siripon Sutthiwanna, Seung-Jun Lee, Woosung Jeon, Dong Sun Lee, Jinsook Ahn, Ryeongeun Cho, H C Park, Seongin Jeong, Hahnbeom Park, Seok-Hyung Bae, Ho Min Kim

    Discovered via OpenAlex

  406. The Biophysicist

    Deep Learning for Proteins Notebook Series Teaches AI for Biomolecular Structure Prediction and Design

    Michael Chungyoun, Gabe Au, Britnie Carpentier, Puvada Sreevar, Courtney Thomas, Jeffrey J. Gray

    Discovered via OpenAlex

  407. Probiotics and Antimicrobial Proteins

    Artificial Intelligence and Protein Design: A retrospective study on 20-year emerging trends and core research areas from bibliometric perspectives

    Wenjuan Zhao, Xiuwu Pan, Wei Yang, Z LIU, Xiyi Wei, Anqi Lin, Bufu Tang, Lin Zhang, Mingjia Xiao, Qing Zeng, Quan Cheng, Weiming Mou, Xiaofan Lu, Kai Miao, Peng Luo, Xingang Cui, Wei Chen

    Discovered via OpenAlex

  408. Bioinformatics

    Evolutionary profiles for protein fitness prediction

    Xiaoran Jiao, S.Q. Lin, Jigang Fan, Zhanming Liang, Weian Mao, Hao Chen, Chunhua Shen

    Discovered via OpenAlex

  409. Journal of Chemical Information and Modeling

    CatIF-RL: Activity-Oriented Enzyme Sequence Design by Steered Inverse Protein Folding

    Yanheng Li, Jialong Xiong, Yuxin Zhang, Tong Cai, Chuan Fu, Shutong Li, Wei Xu, Ruoyi Lyu, Zhaoyang Chen, Zheng Guo, Xinqi Gong, Feng Wang

    Discovered via OpenAlex

  410. AI-Guided Synthetic Protein Sequence Generation for Functional Protein Design Using Gated Recurrent Units (Preprint)

    Pardhasaradhi Padhilam

    Discovered via OpenAlex

  411. iScience

    BoltzOmics: Predicting genetic variant effects on drug binding with Boltz-2

    Khoa Ngo, Kermit L. Carraway III, Colleen E. Clancy, Hajar Amini

    Discovered via OpenAlex

  412. bioRxiv (Cold Spring Harbor Laboratory)

    A Glycan-Aware Diffusion Model for Carbohydrate and Glycoprotein Structure Prediction

    Keshav Sundar, Hyunjun Yang

    Discovered via OpenAlex

  413. Science

    De novo design of orthogonal far-red, orange, and green fluorophore-binding proteins for multiplexed imaging

    Long Tran, Steffen Klein, David Juergens, Shajesh Sharma, Justin A. Decarreau, Gyu Rie Lee, Yujia Wang, Wei Chen, Asim K. Bera, Alex Kang, Jonathan Woods, Emily Joyce, Dionne K. Vafeados, Nicole Roullier, Xinting Li, Bingxu Liu, Bo Yang, Edin Muratspahić, Timothy A. Brown, Jonathan B. Grimm, Ronak H. Patel, Luke D. Lavis, Julia Mahamid, Linna An, David A. Baker

    Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.3 RoseTTAFold-based

  414. Catalysts

    Computational Redesign of Aspartase from Escherichia coli and Its Catalytic Synthesis of β-Alanine

    Long-Xian Li, Bao-Di Ma, Yi Xu

    Discovered via OpenAlex

  415. Nucleic Acids Research

    RNA G-quadruplex structure recognition by chimeric peptides

    Xi Mou, Jiuming Wang, Yanruisheng Shao, Yu Li, Chun Kit Kwok

    Discovered via OpenAlex

  416. bioRxiv (Cold Spring Harbor Laboratory)

    Minimal Data · Maximal Insight (MDMI): A Structure-guided Pipeline for Discovering Functional Alternatives in Peptide-Protein Interfaces

    Pouriya Bayat, Spencer James Perkins, Sebastian Clancy, Sahil Swapnesh Patel, Richard Fei Yin, Krištof Bozovičar, Serena Singh, Suman Shrestha, Zain Moustafa, Riham Zayani, Idorenyin A. Iwe, Sepehr Bayat, Paul Kelly, Justin R. J. Vigar, Vivan Yuna White, Matthew Xie, Mohammad Simchi, Sean Palter, Jessica Nguyen, Ilan Zeisler, Bonny Wu, Keith Pardee

    Discovered via OpenAlex

  417. bioRxiv (Cold Spring Harbor Laboratory)

    Prediction-Guided Design of a More Developable FGF21 Construct

    Çağlar Bozkurt, Evangelia Nathanail, Aniruddh Goteti

    Discovered via OpenAlex

  418. bioRxiv (Cold Spring Harbor Laboratory)

    State-selective inhibition of alpha-synuclein aggregation by de novo oligomer-binding proteins

    Yunxuan Zhang, Hannah L. Han, Lei Ortigosa-Pascual, Uri Z. Miles, Jiapeng Wei, Lexie E. Berkowicz, Finn Snow, Daizheng Tu, Georg Meisl, Shrutika Sansaria, Timothy J. Nott, Heike Laman, Randal Halfmann, Andrew C. McShan, Danny D. Sahtoe, Tuomas P. J. Knowles

    Discovered via OpenAlex

  419. Frontiers in Oncology

    Machine learning-driven identification of DLL3 as a molecular target and development of a DLL3-binding cyclic peptide for glioblastoma

    Dan Xu, Daqing Huang, Zhijie Li, Yan Yan, Zhencun Cui, Zhongfang Zhao, Xiaoju Chen, Maolong Chen, Xiongxiong Liu, Zhaobo Zhou, Qianxi Ni, Taofeng Zhang, Hui Wang, Qi Zeng, Xi’an Xiong, Bin Liu

    Discovered via OpenAlex

  420. Journal of Medicinal Chemistry

    Discovery of Stapled Peptide MYC Degrader with Potent In Vivo Activities for Triple-Negative Breast Cancer Therapy

    Nan Zhang, Xin Li, Yunchen Xu, Yize Jiang, Songyan Gao, Huaxing Shen, Huang Li, Shuai Zhang, Guidong Chi, Bohan Ma, Hongli Liao, Honggang Hu, Si Chen, Xiang Li

    Discovered via OpenAlex

  421. RUNG

    Hands-on session: Nanobody binder design with AI

    Marco Orlando

    Discovered via OpenAlex

  422. bioRxiv (Cold Spring Harbor Laboratory)

    Frozen Protein Foundation-Model Embeddings Improve Antibody–Antigen Binding Affinity Prediction

    Roger Wang, Kevin Jin, Lurong Pan

    Discovered via OpenAlex

  423. bioRxiv (Cold Spring Harbor Laboratory)

    De novo design of selective kinase modulators

    Magnus S. Bauer, Saurav Kumar, Mia S. Donald-Paladino, Dongyang Li, Kody A. Klupt, Matthias Glögl, Ana María Fernández‐Escamilla, Thomas Schlichthaerle, Edin Muratspahić, Xinru Wang, Ludwig Schmiderer, Sebastian Kenny, Brian Coventry, Bulat Faezov, Wei Chen, Alex Shida, Gyu Rie Lee, Yang Hsia, Ryan D. Kibler, Michael B. Elowitz, Daniel Lietha, Behnam Nabet, David A. Baker

    Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.3 RoseTTAFold-based

  424. Frontiers in Bioengineering and Biotechnology

    The limits of sequence-based biosecurity screening tools in the age of AI-assisted protein design

    Bruce J. Wittmann, Nicole E. Wheeler, Steven T. Murphy, Tom Mitchell, Brittany Rife Magalis, Bryan T. Gemler, Kevin Flyangolts, James Diggans, Adam J. Clore, Jacob Beal, Craig Bartling, Tessa Alexanian, Eric Horvitz

    Discovered via OpenAlex

  425. Zenodo (CERN European Organization for Nuclear Research)

    Protein Design from Scratch: De Novo Protein Design via MultiParameter Functional Constraint Integration

    Umair Masood awan

    Discovered via OpenAlex

  426. bioRxiv (Cold Spring Harbor Laboratory)

    Derivatization of the non-ribosomal peptide pyrrolizixenamide using NRPS engineering

    Juliana Effert, Andrea Calderari, Susanna Kremer, Kira J. Weissman, Helge B. Bode

    Discovered via OpenAlex

  427. bioRxiv (Cold Spring Harbor Laboratory)

    Selective miniprotein inhibitors of Aurora-A kinase designed using interaction-motif scaffolding

    Jennifer A. Miles, Bob Schiffrin, James W. Holder, Emily J. Wallis, Iain W. Manfield, Sean Anthony Burnap, Weston B. Struwe, Fanni V. Gergely, Richard W. Bayliss

    Discovered via OpenAlex

  428. Zenodo (CERN European Organization for Nuclear Research)

    Breaking the Bottleneck of Protein Design... Demonstration of Photonic Entropy Computing Optimization

    inquantio

    Discovered via OpenAlex

  429. Journal of Chemical Information and Modeling

    Deep Learning Models Capture Umbrella Sampling-Derived Energetic Trends: A Troponin C Case Study

    Akshaya Narayanasamy, Rocco Moretti, Jens Meiler, Steffen Lindert

    Discovered via OpenAlex

  430. bioRxiv (Cold Spring Harbor Laboratory)

    Structure-guided design of a CD81-binding mini-protein that blocks hepatitis C virus entry

    Sojin An, Eunji Jo, Hee Seong Choi, Sang Soo Kim, Dong Won Kim, Woorim Yang, Sung Key Jang, Kyu-Ho Paul Park, Sang‐Jun Ha, Yong Song Gho, Seong Wook Yang, Seungtaek Kim, Hyun‐Soo Cho

    Discovered via OpenAlex

  431. Zenodo (CERN European Organization for Nuclear Research)

    Evolution of Enzymes, 'Tunneling' Through Instead of Going Over the Wall... Elucidating the Use of Quantum Tunneling in Artific

    inquantio

    Discovered via OpenAlex

  432. Journal of Chemical Information and Modeling

    Scaling SMILES-Based Chemical Language Models for Therapeutic Peptide Engineering

    Aaron L. Feller, Maxim Secor, Sebastian Swanson, Claus O. Wilke, Kristine Deibler

    Discovered via OpenAlex

  433. Journal of Biological Chemistry

    Evolution- and structure-guided redesign of the Stachel motif yields soluble and potent modulators of adhesion GPCRs

    Abibe Useini, Yue Feng, Isabell Kaczmarek, Georg Künze, Doreen Thor, Torsten Schöneberg

    Discovered via OpenAlex

  434. ACS Synthetic Biology

    Microbial Synthesis of Daphnetin by Engineering 2-Oxoglutarate-Dependent Dioxygenases

    Shunmin Ji, Chong Xie, Yue Wang, Mengchu Sun, Jiu Dai, Yong Du, Xiaolin Shen, Jia Wang, Qinggang Yin, Xinxiao Sun, Qipeng Yuan

    Discovered via OpenAlex

  435. Research Square

    Investigating the Effect and Mechanism of Semantic Alignment in Fixed-Backbone Protein Sequence Design

    Ke Zhang

    Discovered via OpenAlex

  436. bioRxiv (Cold Spring Harbor Laboratory)

    The YTHDC1 glutamate-rich domain docks to the ADAR1 Zα Domain, linking the N 6 -methyladenosine modification of pre-mRNAs to dsRNA editing

    Dmitry Gromak, Alexey К. Shaytan, Alan G. Herbert, Maria S. Poptsova

    Discovered via OpenAlex

  437. Al-mağallaẗ al-ʻirāqiyyaẗ li-l-ʻulūm al-bayṭariyyaẗ/Iraqi journal of veterinary sciences

    Evaluation of an M Cell–Targeted FedA Fusion Protein as an Oral Vaccine Candidate for Post-Weaning Diarrhea

    Quoc-Gia Mai, Khoi-Nguyen Le, Hieu Tran‐Van

    Discovered via OpenAlex

  438. BMC Microbiology

    Isolation and genomic analysis of otomycosis pathogens, and genomics-informed antimicrobial peptide design with potential therapeutic applications

    Wenguang Shi, Jiahao Hu, Qingru Jiang, Yan Xu, Rongjie Li, Huihui Xu, Gaoyang Zhang, Ziqi Cui, Ruiyue Ouyang, Wenxuan Wu, Yujie Li, Haiyu Hong, Xiangyu Mou, Wenjing Zhao, Shuli Chou

    Discovered via OpenAlex

  439. In Silico Pharmacology

    Generative AI in antibody engineering: emerging concepts and translational bottlenecks in lung cancer

    Xiaohong An, Fangfang Li, Chao Xia, Yuxia Li, Haonan Li, Fei Xie

    Discovered via OpenAlex

  440. bioRxiv (Cold Spring Harbor Laboratory)

    Computational design of de novo integrated domains enables rational control of pathogen effector recognition in plant NLR immune receptors

    Yuxuan Xi, Angus Bucknell, Joseph L. Watson, Abbas Maqbool, J. R. Bennett, Inna Goreshnik, Dionne K. Vafeados, Michel Sanchez, G. L. Knight, Rafał Zdrzałek, Clemence A. Rodney, Indira Saado, Caroline E. Stone, Emma K Turley, Daniel S. Yu, Amber Gentle, Lauren S. Ryder, Yan Xia, Vincent M. Were, Jonathan G. Heddle, David A. Baker, Peter M. F. Emmrich, Nicholas J. Talbot, Mark James Banfield, Adam R. Bentham

  441. Current Opinion in Structural Biology

    Progress in structure prediction and design of adaptive immune receptors

    Tomer Cohen, Tanya Hochner, Dina Schneidman‐Duhovny

    Discovered via OpenAlex

  442. Zenodo (CERN European Organization for Nuclear Research)

    A Sexagesimal Harmony Algorithm Approach to Hexagonal Ice Suppression

    Jorge Alexander López Miranda

    Discovered via OpenAlex

  443. Protein Science

    RINAMI : Residue‐attributed interpretable neural network for predicting absolute folding free energy by merging structure and sequence information

    Naoki Tomita, George Chikenji

    Discovered via OpenAlex

  444. Protein Science

    Enhancing machine learning‐based binder design with high‐throughput screening: A comparison of mRNA and yeast display technologies

    Zhiyuan Yao, McGuire Metts, Avery K. Huber, J M Li, Tomoaki Kinjo, Henry Dieckhaus, Amrita Nallathambi, Albert A. Bowers, Brian A. Kuhlman

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.3 RoseTTAFold-based

  445. arXiv (Cornell University)

    Variable-Length Generative Protein Design via Generalized Poisson Flow

    Chaoran Cheng, Zhanghan Ni, Yanru Qu, Yuxin Chen, Ruihan Guo, Jiajun Fan, Ge Liu

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.8 Flow-based

  446. Protein Science

    Applications and limitations of AI tools in enzyme design

    Rosa Teijeiro-Juiz, Nina Egeler, Grzegorz Jamróg, Marion Ringel, Thomas Brück, Bruno Di Geronimo, Bernhard Loll

    Discovered via OpenAlex

  447. bioRxiv (Cold Spring Harbor Laboratory)

    Hybrid quantum-classical de novo design of MHC-binding peptides

    Emilie Sofie Engdal, Jonathan Funk, Omar Bacarreza, Laura Machado, Kristoffer Haurum Johansen, Janine Sophie Kemming, Thorin Farnsworth, Valentas Brasas, Rodrigue Yves Louis Lefèvre‐Morand, Mateusz Slysz, Oliver Luscombe Noerregaard, Oliver August Dall’Alba Sandberg, Alexander Makarovskiy, Peter Lodahl, Carlos G. Acevedo‐Rocha, Krzysztof Kurowski, Sine Reker Hadrup, William R. Clements, Timothy P. Jenkins

    Discovered via OpenAlex

  448. bioRxiv (Cold Spring Harbor Laboratory)

    MAERM: Predicting Enzyme-Reaction Matching Relationships with a Mixed-Attention Model

    Tiantao Liu, Silong Zhai, Shaolong Lin, Xinke Zhan, Junwen Deng, Huanxiang Liu, Shirley W. I. Siu

    Discovered via OpenAlex

  449. bioRxiv (Cold Spring Harbor Laboratory)

    Benchmarking AI/ML-Driven PTIm-mAb Across Eleven FDA-Approved Bispecific Antibodies: A Cross-Tool Validation Study

    Murali K. Addepalli, Mahesh Prattipati

    Discovered via OpenAlex

  450. BMC Bioinformatics

    Enhancing tumor T cell antigen prediction by integrating deep protein representations

    Umut Oskay, Baris Tudes, Emre Sefer

    Discovered via OpenAlex

  451. Bioresources and Bioprocessing

    Artificial intelligence and automation in enzyme engineering: evolution, advances, and future perspectives

    Kexin Hao, J C Liu, Hui Tang, Yan Zhang, Yandong Sun, Hongyu Zhang, Ji Wang, Peng Liu, Jianmei Luo, Jing Bo Zhao

    Discovered via OpenAlex

  452. Journal of the American Chemical Society

    A De Novo CO 2 Reductase Featuring a Cysteine-Ligated Cobalt Porphyrin Cofactor

    Emily Radley, Alessia Andrews, Indrek Kalvet, Yunling Deng, Elizabeth L. Bell, Colin Levy, Mary Ortmayer, Derren J. Heyes, Clare F. Megarity, Reyes Núñez‐Franco, Amy E. Hutton, Yi Lu, David A. Baker, Anthony P. Green

    Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.3 RoseTTAFold-based

  453. bioRxiv (Cold Spring Harbor Laboratory)

    Characterising AlphaFold 3’s ability to predict T cell antigen specificity

    Benjamin McMaster, Ali El Moselhy, Ilija Ilievski, Christopher J. Thorpe, Nicole L. La Gupta, Jamie Rossjohn, Charlotte Mary Deane, Hashem Koohy

  454. Biochemistry

    From First Principles to Function: How AI Is Reshaping Enzyme Design

    Sebastian Lindner, Florence J. Hardy, Donald Hilvert

    Discovered via OpenAlex

  455. arXiv (Cornell University)

    DrugGen 2: A disease-aware language model for enhancing drug discovery

    Ali Motahharynia, Mohammadreza Ghaffarzadeh-Esfahani, Mahsa Naghavi Sheikholeslami, Navid Mazrouei, Matin Irajpour, Yousof Gheisari, Hajar Sirous

    Discovered via OpenAlex

  456. arXiv (Cornell University)

    UMA-Inverse: Ligand-Conditioned Protein Inverse Folding with a Distogram-Supervised Dense Pair Encoder

    William Sobolewski

    Discovered via OpenAlex

  457. bioRxiv (Cold Spring Harbor Laboratory)

    Machine learning guided cell-free expression maps the biochemical landscape of carbonic anhydrase

    John Tyler Lazar, Evan Komp, Irene Martinez, Kyle Zolkin, Pascal Notin, Samer Saleh, Grant M. Landwehr, K I Kim, Anru Tian, Benjamin Shapero, Ashty S. Karim, Debora S. Marks, Gregg T. Beckham, Michael C. Jewett

    Discovered via OpenAlex

  458. Advanced Science

    De Novo Designed Minibinders Targeting the GDF15–GFRAL Axis Reverse Cancer Cachexia and Restore Anti‐Tumor Immunity

    Haitao Wang, Tianzhen Hua, Meiling Wang, Bingbing Meng, Yue Zhang, Chengxu Jiang, Yunhe Gao, Hongqi Yang, Jian Bo

    Discovered via OpenAlex

  459. bioRxiv (Cold Spring Harbor Laboratory)

    ThermoFusion: A Multimodal Deep Learning Framework for Generalizable Prediction of Enzyme Thermostability

    Yao Wei, Ivano Eberini, Fabian Meyer

    Discovered via OpenAlex

  460. ACS Applied Bio Materials

    Bioactive Peptides for Oral Diseases: Biomaterial-Assisted Therapeutics and Translational Applications

    Li Zhang, Yang Lin, W Jia, Ruchen Xuan, Jianmin Wu, D Q Wang, Rui Xu

    Discovered via OpenAlex

  461. bioRxiv (Cold Spring Harbor Laboratory)

    Deep-Interact Studio: An Interactive Deep Learning Model Building Platform for Biomolecular Interaction Prediction

    Dipayan Sarkar, K. D. Bardhan, Chiranjib Sarkar

    Discovered via OpenAlex

  462. arXiv (Cornell University)

    Rethinking Benchmarks and Models for Enzyme Specificity Prediction

    Elizabeth H. Mahood, Natália Komorníková, Tomáš Pluskal, Pranam Chatterjee

  463. Zenodo (CERN European Organization for Nuclear Research)

    G-Walk Protein Design: From ISA Programme to Amino Acid Sequence via Orbit Occupancy

    Ian Richard C Buckley

    Discovered via OpenAlex

  464. bioRxiv (Cold Spring Harbor Laboratory)

    CatESO: Differentiable Enzyme Sequence Optimization Guided by Substrate-Aware kcat Prediction

    Zhenjia Gan, Yuzhi Xu, Junde Xu, Z W Wu, J Huang, Jiabin Yin, Guangyong Chen, John Z. H. Zhang

    Discovered via OpenAlex

  465. Theoretical and Natural Science

    From Traditional Protein Engineering to AI-Driven Design: Principles, Methods, and Applications

    Zonghao Cheng

    Discovered via OpenAlex

  466. Biotechnology and Bioengineering

    Developing Anti‐EGFR/Anti‐HER2 Bifunctional Antibody for Solid Tumors by Protein Engineering

    Senem Sen, Aslı Semerci, Mélis Karaca, Recep Erdem Ahan, Cemile Elif Özçelik, Elif Duman, Behide Saltepe, Ebru Aras, Ebru Aras, Eray Ulaş Bozkurt, Hilal Yazıcı, Müge Serhatlı, Urartu Özgür Şafak Şeker

    Discovered via OpenAlex

  467. bioRxiv (Cold Spring Harbor Laboratory)

    Accurate ΔT m Prediction Without Protein Structure Inputs for Biomolecular Stability

    Daniel Siegismund, Mario Wieser, Eriberto Noel Natali, Stephan Steigele

    Discovered via OpenAlex

  468. Molecules

    Bridging Algorithms and Biocatalysis: Perspectives on AI-Supported Enzyme Engineering

    Rosa Teijeiro-Juiz, Thomas Brück, Bernhard Loll

    Discovered via OpenAlex

  469. npj Drug Discovery.

    Generative AI for controllable protein sequence design: A survey

    Yiheng Zhu, Zitai Kong, Jialu Wu, Mingze Yin, Weize Liu, Yuqiang Han, Hongxia Xu, Chang‐Yu Hsieh, Tingjun Hou, Jian Wu

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 4.0 Review · 4.Scaffold to Sequence

  470. bioRxiv (Cold Spring Harbor Laboratory)

    Expanding all-α-helical protein space through rational computational design

    Katherine I. Albanese, Joel J. Chubb, Luis I. Gutierrez-Rus, Xiyue Leng, Kathleen W. Kurgan, Bram Mylemans, Katarzyna Ożga, Rokas Petrenas, Andrey V. Romanyuk, Amanda M. Acevedo‐Jake, Joel Roca‐Martínez, Stephen Cross, J. L. Ross Anderson, Jonathan Clayden, Graham J. Leggett, Jennifer J. McManus, Thomas A. A. Oliver, Christine Anne Orengo, Nigel Shaun Scrutton, Andrew John Wilson, Aimee L. Boyle, Derek N. Woolfson

    Discovered via OpenAlex

  471. arXiv (Cornell University)

    Design-CP: Context Parallelism for Design of Protein Nanoparticles

    Lorenzo Tarricone, Helen E. Eisenach, Aiko Muraishi, Charlotte M. Deane

    Discovered via OpenAlex

  472. Science

    Membrane protein solubilization and structure determination using de novo–designed proteins

    Ljubica Mihaljević, David E. Kim, Pooja Bandawane, Helen E. Eisenach, Andrew J. Borst, Alexis Courbet, Connor Weidle, Kenneth D. Carr, Everton Burlamarque Bettin, Qiushi Liu, Aldo T. Trejos, Sagardip Majumder, Surabhi Kokane, Alexander Stevens, Edin Muratspahić, Thomas Schlichthaerle, Marc Expòsit, Xinting Li, Mila Lamb, A G Murray, Rashmi Ravichandran, Elizabeth C. Williams, Shuyuan Hu, Lynda M. Stuart, Linda Grillová, Nicholas Robert Thomson, Michael Landreh, Pengxiang Chang, Lorenzo Giacani, Melissa J. Caimano, Kelly L. Hawley, Neil P. King, David A. Baker

    Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.3 RoseTTAFold-based

  473. bioRxiv (Cold Spring Harbor Laboratory)

    Linker-Length Landscape Mapping Enables Coupling of Diverse Synthetic Chemically Induced Dimerization Systems to Molecular Readouts

    Yuxin Pan, Shoukai Kang, Davi Nakajima An, Yixuan Yu, Frank DiMaio, Liangcai Gu

  474. Proceedings of the National Academy of Sciences

    Beyond native sequence recovery: Improved modeling of the sequence-energy landscape of protein structures

    Foster Birnbaum, Amy E. Keating

    Discovered via OpenAlex

  475. Chinese Science Bulletin (Chinese Version)

    Advances in the application of artificial intelligencein protein design

    Shengquan Liu, Ruiwen Zhang, Jiong Li

    Discovered via OpenAlex

  476. arXiv (Cornell University)

    Diffeomorphic Optimization

    Ludwig Winkler, Andrew Leaver‐Fay, Joseph Kleinhenz, Pan Kessel

    Discovered via OpenAlex

  477. Cancer Reports

    Investigating the Role of Anti‐Leukemia Inhibitory Factor Antibody on Cytokine Profile in a Mouse Model of Breast Cancer

    Seyed Mohammad Seifati, Hossein Hadinedoushan, Hossein Ansariniya, Fateme Zare

    Discovered via OpenAlex

  478. MedComm

    De Novo Synthesis in Cancer Immunotherapy: Applications and Prospects

    Jie Yang, Yanfeng Wu, Luo J

    Discovered via OpenAlex

  479. Briefings in Bioinformatics

    Intelligent antigen design combined with yeast display enhances targeted immune responses

    Yun-Fei Ma, Guang-Hui Yin, Y L Pan, Ye Liu

    Discovered via OpenAlex

  480. Briefings in Bioinformatics

    FireProtASR 2.0: evolution-guided Design of Protein Ancestors and Successors with phylogenetics and machine learning

    Pavel Kohout, David Lacko, Miloš Musil, Simeon Borko, Martin Stepanek, Jan Velecký, Petr Kabourek, Rayyan Tariq Khan, Monika Rosinska, Jiřı́ Damborský, Stanislav Mazurenko, David Bednář

    Discovered via OpenAlex

  481. ACS Omega

    Rational Design of Peptide Binders Targeting Prominin-1 and Sortilin for Molecular Sensing Applications

    Samavath Mallawarachchi, Nirmitee Mulgaonkar, Samuel B. Mabbott, Shreya A. Raghavan, Sandun Fernando

    Discovered via OpenAlex

  482. Briefings in Bioinformatics

    Mixture diffusion model for multimodal antibody design

    Vasanth Durvasula, Tiara Natasha Binte Sayuti, Jagath Chandana Rajapakse

    Discovered via OpenAlex

  483. Bioinformatics

    Agentomics: an agentic system that autonomously develops novel state-of-the-art solutions for biomedical machine learning tasks

    Vlastimil Martinek, Andrea Gariboldi, Dimosthenis Tzimotoudis, Mark Galea, Elissavet Zacharopoulou, Aitor Alberdi Escudero, Edward Blake, David Čechák, Luke Cassar, Alessandro Balestrucci, Panagiotis Alexiou

    Discovered via OpenAlex

  484. bioRxiv (Cold Spring Harbor Laboratory)

    AI-guided discovery for low-resource peptide engineering using evolutionary scale modeling

    Leo Andrekson, Robin Rydbergh, Rocío Mercado, Michaela Wenzel

    Discovered via OpenAlex

  485. arXiv (Cornell University)

    MolSafeEval: A Benchmark for Uncovering Safety Risks in AI-Generated Molecules

    Tong Xu, Xintong Cao, Z G Zhu, Keyan Ding, Huajun Chen

    Discovered via OpenAlex

  486. Bioinformatics

    LoMuS: low-rank adaptation with sequence multi-representation improves protein stability prediction

    Samuel Infante, Akash Singh, Anowarul Kabir

    Discovered via OpenAlex

  487. Bioinformatics

    PreFold-dG: estimating binding affinity of protein–protein interaction from intermediate representations of protein folding model

    S. J. Park, Soorin Yim, Dongyun Kim, Kiwoong Yoo, Doyeong Hwang, Kyungwook Lee, Jongseong Jang, Kiyoung Kim

    Discovered via OpenAlex

  488. Cell

    Structural basis for host membrane binding and remodeling by invading malaria parasites

    Meseret T. Haile, Daphne A. Kaxiras, James Zhen, Carolyn L. Lee, Britney Jiang, Jennifer L. Small-Saunders, Chi-Min Ho

    Discovered via OpenAlex

  489. Zenodo (CERN European Organization for Nuclear Research)

    Semantic Deconstruction and Operator Reconfiguration: An Architecture of Morphic Computation Based on Inverse Categorical Compilation Theory

    Jincheng Zhang

    Discovered via OpenAlex

  490. Journal of Biomedical Advance Scientific Research

    Artificial Intelligence in Protein Engineering: From Therapeutic Design to Precision Medicine

    Ian Pranandi

    Discovered via OpenAlex

  491. Advance in Biological Research

    Computational Intelligence-driven DPP-4 Inhibitory Peptide Prediction and Bispecific Antibody Design: Integrating Deep Learning, Molecular Dynamics, and Nanodisc Validation

    Taozhi Wang

    Discovered via OpenAlex

  492. International Journal of Molecular Sciences

    Hybrid Approach to Protein–Protein Complex Affinity Prediction Based on Language Models and Molecular Dynamics

    Elizaveta Alexandrovna Bogdanova, Artem V. Chernukhin, Alexey К. Shaytan

    Discovered via OpenAlex

  493. Futuristic Biotechnology

    AI-Designed Synthetic CRISPR Enzymes: Evolving Molecular Scissors Beyond Natural Constraints

    Shaista Khalid

    Discovered via OpenAlex

  494. Molecular Medicine

    Neuroprotective potential of a TrkB-FL-derived cell-penetrating peptide in cochlear synaptopathy and noise-induced hearing loss

    Elena Torres-Campos, Isabel Varela‐Nieto, Margarita Díaz‐Guerra

    Discovered via OpenAlex

  495. bioRxiv (Cold Spring Harbor Laboratory)

    Function-guided design of active enzymes

    Mingyang Hu, Lunjie Wu, Yi Yang, Feiran Li, Linchao Zhu

    Discovered via OpenAlex

  496. bioRxiv (Cold Spring Harbor Laboratory)

    OpenGerminal: an open-source implementation of the Germinal antibody design pipeline

    Bing Han, Sheng Li

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 4.5 GNN-based · 4.Scaffold to Sequence

  497. arXiv (Cornell University)

    Preference-based Antibody Expression Ranking: Scaling with Large-scale Weak Supervision

    Josh Qixuan Sun, Morteza Babaie, Wenyang Hou, Mark Crowley, D R Young

    Discovered via OpenAlex

  498. Zenodo (CERN European Organization for Nuclear Research)

    Protein Secondary Structure Prediction Using ESMFold: A Deep Learning-Based Bioinformatics Web Application

    Tarun G. S, Tarun Sai, Vedant Habbu, Siddharth Holla, Rohan K B

    Discovered via OpenAlex

  499. arXiv (Cornell University)

    Structure-Regularized Interpretable TCR-Epitope Prediction

    Jiarui Li, Zixiang Yin, Yunbei Zhang, Janet Wang, Samuel J. Landry, Zhengming Ding, Ramgopal R. Mettu

    Discovered via OpenAlex

  500. arXiv (Cornell University)

    Modeling Protein Evolution with Generative Models: from Extant Sequence Data to Evolutionary Dynamics

    Matteo Bisardi, Leonardo Di Bari, Saverio Rossi, Karol Buda, Francesco Zamponi, Martin Weigt

    Discovered via OpenAlex

  501. bioRxiv (Cold Spring Harbor Laboratory)

    Loop-Directed Cofactor Binding Enables Programmable Multicofactor Protein Design

    Andrew C. Mutter, Aleksandr Uvaydov, Eskil M. E. Andersen, Sara Morsi, Sarah Beck, Mohammad Khan, Bruce Allan Palfey, Carolyn E. Lubner, Ronald L. Koder

    Discovered via OpenAlex

  502. Amino Acids

    Reprogramming parasitic signatures into anticancer peptide candidates: in silico discovery of Leishmania major-derived peptides

    Abbas Dehghanian, Mohammad Izadi, Zahra Minaei, Mostafa Cheshrokh, Fatemeh Fathi Tadavani, Anahita Masoudi, Mohammad Aref Bagherzadeh, Mirza Ali Mofazzal Jahromi, Majid Pirestani

    Discovered via OpenAlex

  503. bioRxiv (Cold Spring Harbor Laboratory)

    Prosculpt: Lowering the Barrier to Computational Protein Design

    Federico Olivieri, Alina V. Konstantinova, Neža Ribnikar, Nej Bizjak, Žan Žnidar, Kiyan Abel, Eva Rajh, Ajasja Ljubetič

    Discovered via OpenAlex

  504. Preprints.org

    A Linguistic Model for Protein Structure Generation

    Aashish Ashok Pattar, Deepesh Nagarajan

    Discovered via OpenAlex

  505. Journal of dental hygiene science

    Antimicrobial and Antibiofilm Activities of Allomyrinasin against Streptococcus mutans

    Hye Young Mun, Yeeun Han, Song-Mi Choi, Sung-Min Kim, Jung Yun Kang

    Discovered via OpenAlex

  506. Nature Communications

    Mechanistic insights into modulation of productive substrate accessibility for efficient PET depolymerization

    Dongwoo Ki, Jiyoung Park, Hwaseok Hong, Hogyun Seo, Beomsu Kim, Hyeonwoo Hwang, Kyung‐Jin Kim

    Discovered via OpenAlex

  507. International Journal of Innovative Technologies in Social Science

    ERENUMAB, A NEW PREVENTIVE TREATMENT FOR MIGRAINE: MECHANISM OF ACTION, SAFETY AND EFFICACY

    Mikołaj Jońca, Natasza Kurys, Mikhail Kazachok, Szymon Paruszewski, Julia Kupczak, Aleksandra Dybcio, Katarzyna Kupczyk, Dorota Szydłowska, Adam Kubisa, Mateusz Miluski

    Discovered via OpenAlex

  508. npj Science of Food

    De novo design and experimental characterization of bitter peptides

    Alexandra Steuer, Francesco Ferri, Laura Eckrich, Julia Heidenkampf, Verena Karolin Mittermeier-Kleßinger, Silvia Schaefer, Maik Behrens, Noelia Ferruz, Corinna Dawid, Antonella Di Pizio

    Discovered via OpenAlex

  509. Nature

    Zero-shot design of drug-binding proteins via neural iterative selection−expansion

    Benjamin N. Fry, Kaia Slaw, Nicholas F. Polizzi

  510. International Journal of Molecular Sciences

    Thermostability Engineering in Therapeutic Antioxidant Enzymes: From Molecular Fundamentals to Oxidative Stress Applications

    Diana Tatarciuc, Irina Mihaela Esanu, Iolanda Foia, Mioara-Florentina Trandafirescu, Teodor Flaviu Vasilcu, Dragos Catalin Ghica, Magda Ecaterina Antohe, Adina Oana Armencia, Roxana-Ionela Vasluianu

    Discovered via OpenAlex

  511. bioRxiv (Cold Spring Harbor Laboratory)

    ComplexDesign: sequence-hallucination design of protein binders bridging multiple proteins

    J Q Xu, Milong Ren, Ning Qi, Xinru Zhang, Zaikai He, Chungong Yu, Dongbo Bu

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 2. Model-based design · 2.1.1 trRosetta-based

  512. bioRxiv (Cold Spring Harbor Laboratory)

    Computational Redesign of an Antifreeze Protein Using Deep Learning

    Cianna N. Calia, Arthur J. Altunc, Rosemary J. Eufemio, Benjamin O. Alvarado, Jake D. Huynh, Eunkeu Oh, Michael D. Burkart, Konrad Meister, Francesco Paesani

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 4.5 GNN-based · 4.Scaffold to Sequence

  513. Biochemistry

    Targeting the WASF3 Regulatory Complex in Pancreatic Cancer Using Stapled Peptides

    Taylor C. Dill, Elliot J. Alger, Sophia Gambale, Eileen J. Kennedy

    Discovered via OpenAlex

  514. Bioinformatics

    De novo epitope-specific antibody design via time-dependent guidance

    Yunji Kim, Minkyung Baek

    Discovered via OpenAlex

  515. Trends in Food Science & Technology

    Rational design of oil crop-derived protein nanofibrils: An AI-driven solution for process control and functional prediction

    Chaoting Wen, Jieyu Wang, Guoyan Liu, Jixian Zhang, Lingjun Tong, Xin Xu

    Discovered via OpenAlex

  516. bioRxiv (Cold Spring Harbor Laboratory)

    Orally available designed miniproteins inhibit enterotoxigenic Bacteroides fragilis pathology by blocking toxin receptor binding

    Pooja Srinivas, Victor Adebomi, Susan M. Markiewicz, Kang Wang, Denise Chac, Kristofer Lindenauer, Nishoni Huber, Zhi‐Hang Tao, Phat Luong, Stephen Rettie, ML Smith, Asim K. Bera, Alex Kang, Hannah Nguyen, Maika Schneider, Y Y Wang, Snow Brook Peterson, Min Dong, Ana A. Weil, Ana A. Weil, Joseph D. Mougous

  517. arXiv (Cornell University)

    Scalable Peptide Design via Memory-Efficient Equivariant Transformer

    Rui Jiao, Xiangzhe Kong, Yinjun Jia, Yijia Zhang, Ziyi Yang, Yang Liu, J Y Ma

    Discovered via OpenAlex

  518. Computers in Biology and Medicine

    Sequence–structure cross-attention model integrating ESM-2 embeddings and AlphaFold cues for accurate prediction of Escherichia coli protein solubility

    Z. Elmi

    Discovered via OpenAlex

  519. bioRxiv (Cold Spring Harbor Laboratory)

    Multi-Scale Machine Learning for Antibody-Antigen Binding Affinity Prediction Using Deep Mutational Scanning and Structural Features

    Santhosh Sivasubramani

    Discovered via OpenAlex

  520. bioRxiv (Cold Spring Harbor Laboratory)

    A complete RXFP1–relaxin interaction model unlocks the design of potent mini-protein modulators

    Janik Clément, Tim Lkhagvajargal, Bradley L. Hoare, Tiffany Myint, Daniel Fox, Chunxiao Wang, Gavin J. Knott, Ross A. D. Bathgate, Rhys Grinter

    Discovered via OpenAlex

  521. ScholarsArchive (Brigham Young University)

    Advancing Data Usability, Activity Modeling, and Stability Optimization in Computational Enzyme Design

    Spencer Gardiner

    Discovered via OpenAlex

  522. Bioinformatics

    Optimizing protein design through uncertainty-weighted steering of protein language models

    Alif Bin Abdul Qayyum, Yingtong Zhou, Xiaoning Qian, Byung-Jun Yoon

    Discovered via OpenAlex

  523. Biomacromolecules

    Membrane-Coated Microsphere Functionalization with Polypeptides

    Christopher J. Randolph, Sneha Bhat, Eva de Alba

    Discovered via OpenAlex

  524. arXiv (Cornell University)

    Reduced-Alphabet QUBO/Ising Formulation for Constraint-Driven Cyclic Peptide Sequence Design

    Yan Zhou, Yuqi Wang, Xin Li

    Discovered via OpenAlex

  525. Angewandte Chemie

    Enhancing Enzyme Activity With Mutation Combinations Guided by Few‐Shot Learning and Causal Inference

    Lin Guo, Xiaoguang Yan, Yali Lu, Shengxin Nie, Mingyue Ge, Y R Li, Weiguo Li, Li Zhang, Dongmei Liang, Yihan Zhao, Hongxiao Tan, X S Chen, Shilong Fan, Yefeng Tang, Shengli Wang, Boxue Tian

    Discovered via OpenAlex

  526. International Journal of Applied Technology in Medical Sciences

    Artificial Intelligence in Drug Discovery and Development: Applications, Impact, and Challenges

    Mariana Costa, Hassan Al-Khaled, Oliver Brown, Sakura Yamamoto, Kwame Mensah

    Discovered via OpenAlex

  527. International Journal of Emerging Research in Engineering Science and Management

    Deep Learning Models for Protein Structure Prediction: A Comprehensive Survey

    C Srushti, P M Prathibhavani, K R. Venugopal

    Discovered via OpenAlex

  528. Communications Biology

    Ovo, an open-source ecosystem for de novo protein design

    David Příhoda, Marco Ancona, Tereza Calounova, Adam Kral, Lukas Polak, Hugo Hrbáň, Nicholas J. Dickens, Danny A. Bitton

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.3 RoseTTAFold-based

  529. Probiotics and Antimicrobial Proteins

    Novel Anti-Microbial Peptides Design and Screening Against the KatG Using Molecular Docking and MD Simulation

    Kanchan Mehta, Shama Mujawar, Kumar Gaurav, Ashish Vyas

    Discovered via OpenAlex

  530. Responsive materials

    Peptide‐based antibacterial nanoplatforms: Design principles, stimuli‐regulated behaviors, and applications

    Peng Tan, Chenlong Zhou, Shuaikang Yang, Zhenduo Chen, Guanghui Zhao, Qi Tang, Haoyu Yan, Feng Li, Xi Ma

    Discovered via OpenAlex

  531. arXiv (Cornell University)

    Computationally guided modifications of CviUPO to improve catalytic activity

    Hanna-Friederike Poggemann, Tim Dirks, Timo Jacob, Christoph Jung

    Discovered via OpenAlex

  532. Nature Communications

    SplitSeek-Pro: accurate prediction of splittable sites on protein structures

    Yue Wang, Fengyi Jiang, Tingjie Xu, Lan-Xin Xing, Yajie Liu, Zhiwei Nie, Jie Chen, Wenbin Zhang

    Discovered via OpenAlex

  533. Targeting FABP4 in treating atherosclerosis and metabolic disorders: from mechanism to therapies

    Lin Jiang, Suowen Xu

    Discovered via OpenAlex

  534. ChemRxiv

    The Good, The Bad, and The Ugly of Antibody Design: A Roadmap for Integrating Co-folding with Absolute Binding Free Energy Calculations

    Amogh Sood, Punit K. Jha, Sheenam Khuttan, Dominic A. Rufa, Benjamin J. Shields, Alexander C. Brueckner, Zane Beckwith, Andrea Bortolato, Mary Pitman

    Discovered via OpenAlex

  535. Journal of Agricultural and Food Chemistry

    Systematically Engineering Escherichia coli for Efficient and Complete Hydroxytyrosol Biosynthesis

    Yanting Chen, Qihang Chen, Yajuan Su, Weizhu Zeng, Zilong Dong, J Li, Jingwen Zhou

    Discovered via OpenAlex

  536. Chemical Reviews

    Membrane Protein Design: From Reprogramming Functions to AI-Guided De Novo Design Approaches

    Jefferson Roberts, Patrick Barth

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 1. Reviews · 1.1 De novo protein design

  537. Advanced Science

    A Phase‐Resolved Geometric Deep Learning Framework Maps Structural Determinants of Disease‐Associated Protein Aggregation and Guides Suppressor Design

    Jia Shen Sio, Wei Xuan Wilson Loo, Yan Shan Loo, Wen Xin Tan, Hui Xuan Lim, H Liu, Chen Seng Ng

    Discovered via OpenAlex

  538. Nature Communications

    Sequence redesign of glycosyltransferases for enhanced heterologous expression and glycosylation efficiency in Escherichia coli

    Shanshan Zhang, Yilei Han, Yujing Ding, Xiaofan Lin, Zhipeng Yuan, Xinxiao Sun, Qipeng Yuan, Zheng Liu, Yifei Zhang

    Discovered via OpenAlex

  539. Biosensors

    The Fragmented Nature of Biosensor Development: Challenges and Paths to Mitigation

    Gil Zimran, Assaf Mosquna

    Discovered via OpenAlex

  540. Biochemistry

    Improved Stability and Brightness Following Iterative Redesign of a De Novo Biliprotein

    Felix S. Morey-Burrows, Tingxiang Yang, Woody Ahern, David A. Baker, Andrew Hitchcock, Graham J. Leggett, Jenny Clark, Aneika C. Leney, Christopher Neil Hunter

    Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.3 RoseTTAFold-based

  541. Proteins Structure Function and Bioinformatics

    Physics‐Based Energy Functions for Computational Protein Design

    Thomas Gaillard

    Discovered via OpenAlex

  542. bioRxiv (Cold Spring Harbor Laboratory)

    Differences between protein fitness models can be used to design variants of altered specificity

    Samuel P. Berry, Rachelle Gaudet, Debora S. Marks

    Discovered via OpenAlex

  543. Journal of Pharmaceutical Innovation

    Smart Peptide Design of a Novel Melittin-Based Inhibitor of Tyrosinase and MITF Using Machine-Learning Techniques

    P. Manjusha Govindh, Avinash Mishra, Manoj Kumar Tembhre

    Discovered via OpenAlex

  544. arXiv (Cornell University)

    Pepti-Agent: An AI Agent for Peptide Design and Optimization

    Houxu Chen, Achuth Chandrasekhar, Amir Barati Farimani

    Discovered via OpenAlex

  545. bioRxiv (Cold Spring Harbor Laboratory)

    MAHLER: Integrating Metadynamics and Inverse Folding to Predict Antibody-Antigen Kinetics

    Da Teng, Mary Pitman, Punit K. Jha, Amogh Sood, Dominic A. Rufa, Kevin Ryczko, Andrea Bortolato, Pratyush Tiwary

    Discovered via OpenAlex

  546. bioRxiv (Cold Spring Harbor Laboratory)

    Controlling metal-carbonate phase, form, and function through de novo protein design

    Paul S. Kwon, Xinqi Li, Le Tracy Yu, Harley Pyles, Todd H. Lewis, Connor Weidle, Andrew J. Borst, Catherine Bodinger, Alex Kang, Hannah Nguyen, Johnny Mendoza, Kenneth D. Carr, Brian Coventry, Yang Hsia, Zsombor Molnár, Dongsheng Li, Bo Zhang, Brandi Michelle Cossairt, Shuai Zhang, Asim K. Bera, James J. De Yoreo, David A. Baker

    Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.4 CNN-based

  547. bioRxiv (Cold Spring Harbor Laboratory)

    EditorForge: An Active-Site-Aware Framework for Inverse-Folding-Based Protein Redesign

    Anthony Chen, Jibraan Siddiqui, William Taucar, Leo Tiralongo, Maxim Tkachenko, Andy Xu, Sehaj Bawa, Sihan Guo, Owen Pinska, Jonathan Rim, Joshua Shi, Michael Wang, Eason Zhao

    Discovered via OpenAlex

  548. Scientific Reports

    Entropy quantum computing for fixed-backbone protein design

    Babak Emami, Wesley Dyk, David Haycraft, Jenn Robinson, Lac Nguyen, Mohammad‐Ali Miri, David J. Huggins

    Discovered via OpenAlex

  549. bioRxiv (Cold Spring Harbor Laboratory)

    VFUSE: Virulent Feature Understanding with Sparse autoEncoders

    Michael Yu, Matthew L. Olson

    Discovered via OpenAlex

  550. arXiv (Cornell University)

    EasyNano: rapid epitope-targeted nanobody CDR design via differentiable distogram optimization with ESMFold2

    Yue Hu, Wanyu Cheng, Junqing Wang, Yingchao Liu

    Discovered via OpenAlex

  551. Scientific Reports

    Microwave-induced modulation of intracellular distribution of peptides based on mitochondrial targeting sequences

    Fumihiro Kayamori, Takuto Kariya, Momo Hirata, Yonejiro Arimoto, Tamaki Endoh, Nobuhiro Nakanishi, Kenji Usui

    Discovered via OpenAlex

  552. arXiv (Cornell University)

    APCyc: Property-Informed Design of Cyclic Peptides via Automated Cyclization

    Yifan Zhao, Lang Qin, Jintai Chen

    Discovered via OpenAlex

  553. bioRxiv (Cold Spring Harbor Laboratory)

    DeePEn-A Depth sensitive benchmark for Protein Engineering

    Robert Schmirler, Maurice Brenner, Sebastian Franz, Michael Heinzinger, Burkhard Rost

    Discovered via OpenAlex

  554. bioRxiv (Cold Spring Harbor Laboratory)

    Viability of engineered AAVs via protein language models

    Mélissa Desrosiers, Tommaso Ocari, Jeanne Trinquier, Emilia A. Zin, Timothé Van Meter, Maelle Delmas, Muge Tekinsoy, Arthur Planul, Takahiro Nemoto, Deniz Dalkara, Ulisse Ferrari

    Discovered via OpenAlex

  555. Nature Communications

    Synthetically designed anti-defense proteins overcome barriers to bacterial transformation and phage infection

    Jeremy Garb, David William Adams, Eliane Hadas Yardeni, Melanie Blokesch, Rotem Sorek

    Discovered via OpenAlex

  556. PLoS ONE

    Structural bioinformatic studies of eight integral transmembrane NADPH oxidases and their AlphaFold 3 predicted QTY analogs with reduced hydrophobicity

    Tutu Hu, Rick Cheng, Edward Chen, Shuguang Zhang

    Discovered via OpenAlex

  557. bioRxiv (Cold Spring Harbor Laboratory)

    Active Learning–Guided Peptide Design for Modulating Condensate Properties upon Recruitment

    Kumar Gaurav, Rodrique G. M. Badr, Arya Changiarath, Vasileios A. Xenidis, Lukas S. Stelzl

    Discovered via OpenAlex

  558. bioRxiv (Cold Spring Harbor Laboratory)

    Promera: a unified model for biomolecular structure prediction, filtering, and design

    Bowen Jing, Mihir Bafna, Daniel J. Diaz, Adam R. Klivans, Bonnie Berger

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.2 Diffusion-based

  559. Proceedings of the National Academy of Sciences

    Void-X: A generative void-filling model for predicting atomic packing in proteins

    Jie Yang, Junying Yuan, James J. Chou

    Discovered via OpenAlex

  560. Advanced Science

    Discriminator‐Guided Inverse Folding for Multi‐Property Protein Design

    Yuchuan Zheng, C Liu, Zhaoming Liu, Mao Su, Chenyu Tang, Xiang Zheng, Hao Zhang, Li J

    Discovered via OpenAlex

  561. bioRxiv (Cold Spring Harbor Laboratory)

    Porphyrin-driven redox tuning in structurally defined de novo heme proteins

    Cam Mellor, Christopher Williams, Ethan L. Bungay, Jessica C. Berrones‐Reyes, Rob Barringer, Catherine R. Back, Paul M. Molinaro, Ronald L. Koder, Bruce R. Lichtenstein, Adrian John Mulholland, Matthew P. Crump, J. L. Ross Anderson

    Discovered via OpenAlex

  562. Scholar Commons (Santa Clara University)

    Interpretable Protein Design for Thermostable Antibody Fragments

    Neel Mukkavilli, Konstantin Ivanov, Luis Zamudio, Alex Giannopoulos

    Discovered via OpenAlex

  563. Nature Reviews Bioengineering

    Multi-objective antibody design and optimization using machine learning

    Yun‐Huai Kuo, Chloe N. Brown, Ece Akin, Yunxuan Xie, Peter M. Tessier

    Discovered via OpenAlex

  564. ChemRxiv

    The road to computationally designed artificial metalloenzymes

    Elinor Morris

    Discovered via OpenAlex

  565. Materials Today Bio

    De novo design of dual-target mini-binders simultaneously neutralizing Streptococcus equi subspecies zooepidemicus M-like protein and host TNFR1 confers complete protection against lethal infection

    Ke Ming, Yang Hu, Banbin Xing, Meiting Chen, Yuhua Chen, Xiujuan Chen, Miaomiao Geng, Zhiyong Wu, Yanxia Liu, Lin Wei, Jun Weng, Zigong Wei

    Discovered via OpenAlex

  566. arXiv (Cornell University)

    Active Flow Expansion for Out-of-Distribution Discovery: from Theory to Molecules

    Riccardo De Santi, Bruce Lee, C. Jensen, Kimon Protopapas, Sophia Tang, Cheng-Hao Liu, Pranam Chatterjee, Yisong Yue, Andreas Krause

  567. bioRxiv (Cold Spring Harbor Laboratory)

    Inherent limitations of zero-shot mutation prediction in protein engineering

    Phillip R. Woolley, Aaron L. Feller, Andrew D. Ellington, Claus O. Wilke

    Discovered via OpenAlex

  568. bioRxiv (Cold Spring Harbor Laboratory)

    pLM-Guided Inverse Folding for Antibody Sequence Design

    Valentin Noske, Felix Koulischer, Kathleen Marchal D, Thomas Demeester

    Discovered via OpenAlex

  569. arXiv (Cornell University)

    Constraint-Aware Optimization for Robust Protein Stability Prediction

    A Shivram, Aneesh Sreevallabh Chivukula, Manik Gupta, Sourav Chowdhury

    Discovered via OpenAlex

  570. PLoS Computational Biology

    Heuristic multi-site optimization for protein sequence design using Masked Protein Language Models

    Lijuan Wang, Yuze Wang, Qiu Chen, Li Xiao, Xianliang Liu, Junjie Chen

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 7. Other tasks · 7.1 Effects of mutation & Fitness Landscape

  571. Molecules

    Integrating Single-Cell Profiling with Generative AI for De Novo Design of MMP9 Protein Binders in Diffuse Large B-Cell Lymphoma

    Ziyang Miao, Siyi Zhu, LiWei Qin, Dawei Ma, Mingyang Lai, Pingping Xu, Yaping Jin, Huimin Cai, Shuai Zhao, Yue Wang

    Discovered via OpenAlex

  572. International Journal of Research and Review

    Artificial Intelligence and Large Language Models in Drug Discovery and Pharmacogenomics: A Comprehensive Pharmacological Review of AlphaFold, Generative AI for De Novo Design, Clinical Decision Support, and the Translational Pipeline

    Adiba Begum, Dr. R. L. Manisha, Muvvala Sudhakar

    Discovered via OpenAlex

  573. Stanford Digital Repository

    Towards Energetics-Based de novo Enzyme Design: Elucidating Enzymatic Reactions and Estimating Their Activation Barriers Using Machine-Learned Force Fields

    Gabriel Greenstein, Felipe H. da Jornada, Grant M. Rotskoff, David A. Baker

  574. bioRxiv (Cold Spring Harbor Laboratory)

    Systems-Scale Structural Modeling Reveals the Germline Architecture of Immunodominance

    Ellen L. Shrock, Eric Sun, Amrita Dhindsa, Max H. Witwer, Zhou Yu, Danton Ivanochko, I‐Hsiu Lee, Brian Coventry, Maria Borras Gonzalez, Jean‐Philippe Julien, Stephen Joseph Elledge, David A. Baker

  575. Current Opinion in Biotechnology

    Bacteriophage nanoparticles: an emerging modular delivery platform

    Linzi Whiley, Hannah X. Zhu, Alfonso E. Garcia‐Bennett, Paul R. Jaschke

    Discovered via OpenAlex

  576. bioRxiv (Cold Spring Harbor Laboratory)

    Language Modeling Materializes a World Model of Protein Biology

    Salvatore Candido, Thomas Hayes, Alexander Derry, Roshan Rao, Zeming Lin, Robert Verkuil, Bryan Z. Wu, Jin Sub Lee, Elise S. Bruguera, Jehan A. Keval, Mykhailo Kopylov, John E. Pak, Wesley C. H. Wu, Neil Thomas, Samson J. Mataraso, Alvin Hsu, Ashton Trotman‐Grant, Kilian Fatras, Allan dos Santos Costa, Rohil Badkundri, Halil Akin, Deniz Oktay, Jonathan Deaton, Elizabeth A. Montabana, Hrishita Sitwala, Yue Yu, Marius Wiggert, Dylan Alexander Carlin, Anthony W. Goering, Tomasz Blazejewski, McCullen Sandora, Michael Hla, Tina Z. Jia, Leon H. Kloker, Nicholas Sofroniew, Masatoshi Uehara, Jaspreet Pannu, Sharrol T. Bachas, Daniel S. Liu, Tom Sercu, Alexander W. Rives

    Discovered via OpenAlex

  577. Journal of the American Chemical Society

    Highly Stable Mn(V)-Nitrido and Nitrogen-Atom Transfer Reactivity within a de Novo Protein

    Jithin Thomas, Sudha Yadav, Paul H. Oyala, Veronica Carta, Alec H. Follmer, David Philip Goldberg, Samuel I. Mann

    Discovered via OpenAlex

  578. Zenodo (CERN European Organization for Nuclear Research)

    A Formally Verified, Causality‑Driven Platform for De Novo Antibody Design and Protein Function Prediction

    Igor Ganibaev

    Discovered via OpenAlex

  579. ACS Sensors

    Modular Input–Output Biosensor Design Using De Novo Protein Switches

    James Wang, Julie Yi-Hsuan Chen, Chenggang Xi, Estrella Arteage-Organiz, Andy Hsien-Wei Yeh

    Discovered via OpenAlex

  580. Frontiers in Microbiology

    Optimizing phage therapy with antidefense proteins acquired from the environment

    Ritam Das

    Discovered via OpenAlex

  581. Current Opinion in Biotechnology

    Artificial intelligence tools for enzyme engineering and metabolic engineering

    Michael Volk, Vishal Kaushik Pillalamarri, Ruihan Guo, Ge Liu, Huimin Zhao

    Discovered via OpenAlex

  582. Chemical & Engineering News

    Exclusive: Lundbeck taps Cradle for antibody design

    Rowan Walrath

    Discovered via OpenAlex

  583. Journal of the American Chemical Society

    De Novo Design of Near-Infrared Fluorescence-Activating Proteins

    Yulai Liu, Bernardo Assein Arús, Kanuj Mishra, Taolin Wang, Kun Zhang, Michael Luciano, Venu G. Bandi, Akaash Kumar, Ziyu Guo, Yun Guan, Matthew J. Bick, Miaomiao Xu, Jakob G. P. Lingg, Jessica Bae, Alex Kang, Stacey Gerben, Asim K. Bera, Joshua C. Vaughan, James D. Manton, Emmanuel Derivery, Martin J. Schnermann, André C. Stiel, Oliver T. Bruns†, Chunfu Xu, David A. Baker

  584. Zenodo (CERN European Organization for Nuclear Research)

    Cross-Validation of Three Neural Network Potentials for MMP-1 Zn Active-Site Inhibitor Ranking: A Computationally-Driven Repositioning Study of Vorinostat and Indapamide

    Cheongwoo Han

    Discovered via OpenAlex

  585. ChemRxiv

    An enzymology oriented protein virtual screening software - WhatCat

    Erik N. A. Sundén, Per‐Olof Syrén

    Discovered via OpenAlex

  586. Molecular Cancer

    Landscape of T-cell bispecific antibodies in cancer therapy: therapeutic strategies, challenges and future prospection

    Guanda Jiao, Hongsen Peng, Yiqi Yang, Yang Liu, Xiaoxi Liu, Yuanjia Hu, Yeneng Dai, Z Li, Qi Zhao

    Discovered via OpenAlex

  587. Seminars in Thrombosis and Hemostasis

    Designing the Future of Hemostasis

    Thomas David Daniel Kazmirchuk, Jiashu Wang, Janice Corbette, Zein Al Abideen Hammad, Maha Othman, Ashkan Golshani

    Discovered via OpenAlex

  588. arXiv (Cornell University)

    AgentPLM: Agentic Protein Language Models with Reasoning-Augmented Decoding for Protein Sequence Design

    Sahil Rahman, Maxx Richard Rahman

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 5.4 Transformer-based · 5.Function to Sequence

  589. Food Science and Human Wellness

    AI-Guided Protein Engineering Unlocks DON-degrading Enzyme Thermal Stability via a Loop-to-β-Sheet Conformational Switch

    Qingwei Jiang, Huibing Chi, Jiafeng Niu, Jiahao Liu, H G Zhu, Bin Ma, Ping Zhu, Fengxia Lü

    Discovered via OpenAlex

  590. Journal of Chemical Theory and Computation

    Integrating Conformational Sampling and Siamese Learning to Predict Mutation-Induced Binding Affinity Changes in Abelson Tyrosine Kinase and Its Ligands

    Liangxu Xie, Teng Ma, Xiaohua Lu, Dawei Zhang, Lei Xu, Mingjun Yang, Young-Seob Jeong, Shan Chang, Xiaojun Xu

    Discovered via OpenAlex

  591. Bioinformatics

    PMGen: from peptide-MHC structure prediction to peptide generation

    Amirhossein Hajialiasgary Najafabadi, Amirreza Aleyasin, Jonas Arne Mehl, Salman Soleiman Fallah, Hasmig Aintablian, Burkhard Ludewig, Michele Mishto, Juliane Liepe, Johannes Söding

    Discovered via OpenAlex

  592. bioRxiv (Cold Spring Harbor Laboratory)

    Antibody maturation increases rigidity in protein-contacting regions and flexibility at glycan interfaces

    Shahlo O. Solieva, Joyce Park, Justin J. Miller, Austin Kriews, Amelia Escolano, Gregory R. Bowman

    Discovered via OpenAlex

  593. Applied Science and Biotechnology Journal for Advanced Research

    Deep Learning for Protein Structure Prediction: From AlphaFold to the Next Frontier

    Everest Shiwach, Sandeep Kumar

    Discovered via OpenAlex

  594. International Journal of Drug Delivery Technology

    From Monoclonal to Multifunctional: The Evolving Landscape of Engineered Antibodies

    Kamali M L, Tha Thayuamanavan, Preethi Vardhana S, Sultan Mohaideen H, Dimpal N, Hashika SK

    Discovered via OpenAlex

  595. bioRxiv (Cold Spring Harbor Laboratory)

    Comparison of AI protein structure ensemble prediction tools

    Lisa Otten, Jeremy M. G. Leung, Lillian T. Chong, Daniel M. Zuckerman

    Discovered via OpenAlex

  596. International Journal of Pharmaceutical Sciences and Drug Research

    Decade of AI in Drug Discovery: Hype or Reality?

    Leela Laroia

    Discovered via OpenAlex

  597. arXiv (Cornell University)

    mRNAutilus: Multi-Objective-Guided Discrete Generation of mRNA with Optimized Therapeutic Properties

    Sawan Patel, Sophia Tang, Yesol Kim, Yinuo Zhang, Divya Srijay, Ping-Jung Lin, Shambhavi Shubham, Fengmei Pi, Cedric Wu, Sherwood Yao, Pranam Chatterjee

  598. bioRxiv (Cold Spring Harbor Laboratory)

    Programmable DNA integration with New-to-Nature tools using Computational Protein Design

    Hailey M. Wallace, Seong Guk Park, Adam T. Smiley, Tuba Sevik, Shubham Dubey, Shirin Fatma, Chau-Duy-Tam Vo, Ethan Creed, Alexandre Zanghellini, Elizabeth H. Kellogg

    Discovered via OpenAlex

  599. PubMed

    SwitchCraft: A Programmatic Framework for Designing State-Switching Proteins

    Bowen Jing, Mihir Bafna, Anisha Parsan, Heyuan Michael Ni, David Kwabi-Addo, Bryan D. Bryson, Adam Klivans, Bonnie Berger

    Discovered via OpenAlex

  600. Journal of Medicinal Chemistry

    Structure-Guided Grafting of Cell-Penetrating Motifs into Stapled Peptides for Intracellular PPI Inhibition

    Minami Fujita, Tsuyoshi Konuma, Ayaka Yoshida, Noriaki Arakawa, Kosuke Saito, Yosuke Demizu

    Discovered via OpenAlex

  601. Nature Reviews Bioengineering

    Applying therapeutic peptide design principles to agricultural peptides

    Jack H. Cobon, David J. Craik, Conan K. L. Wang

    Discovered via OpenAlex

  602. arXiv (Cornell University)

    AMix-2: Establishing Protein as a Native Modality in Large Language Models

    Keyue Qiu, Yixin Wu, Lihao Wang, Yawen Ouyang, Jixiang Yu, Zihan Zhou, Changze Lv, Dongyu Xue, Yuxuan Song, Xinbo Zhang, Hao Wang, Jiangtao Feng, Zhiqiang Gao, Lijun Wu, Xiaoqing Zheng, Ka‐Chun Wong, Lei Bai, Ya-Qin Zhang, Wei‐Ying Ma, Dahua Lin, Bowen Zhou, Hao Zhou

    Discovered via OpenAlex

  603. Nature Communications

    A T7 RNAP regulatory toolbox for cell-free network engineering and biosensing applications

    Pao‐Wan Lee, Seyed Saeed Mottaghi, Matthis Guillaume Lugnier, Sebastian J. Maerkl

    Discovered via OpenAlex

  604. Physical Review Applied

    Designing lattice proteins with variational quantum algorithms

    Anonymous, Lucas Knuthson, Anders Irbäck, Sandipan Mohanty, Laura García-Álvarez, Göran Johansson

    Discovered via OpenAlex

  605. bioRxiv (Cold Spring Harbor Laboratory)

    Objective curriculum-guided design of multi-property proteins

    Longying Liu, Jianquan Zhao, Xiaomin Xie, Simeng Xu, Milong Ren, Xinru Zhang, Zaikai He, Fan Liu, Chungong Yu, Kun Wang, Xinglong Wang, Xinmiao Liang, Xianlong Ye, Dongbo Bu, Han Zhou

    Discovered via OpenAlex

  606. Preprints.org

    Programmable Icosahedral Protein Nanocages: A De Novo Design Framework for Reducing Kinetic Mis-Assembly and Enhancing Experimental Assembly Fidelity

    Ashfaq Hussain

    Discovered via OpenAlex

  607. The Canadian Journal of Chemical Engineering

    Nano‐enzyme engineering: Advancing enzyme immobilization for industrial and environmental applications

    Muhammad Irfan, Shamsa Shabbir, Wajiha Ali, Muhammad Amir, Arslan Shafi, Shahida Hameed, Shoukat Sajad, Muhammad Rafiq

    Discovered via OpenAlex

  608. arXiv (Cornell University)

    Computational Modeling of Antibody-Antigen Complexes: PLM-Based and MSA-Based Approaches

    Xiao Luo

    Discovered via OpenAlex

  609. bioRxiv (Cold Spring Harbor Laboratory)

    Affinity Fine-Tuning of Boltz-2: An Open Framework for Protein-Ligand Potency Prediction in Drug Discovery

    Samad Amini, Simone Sciabola, Ye Wang

    Discovered via OpenAlex

  610. BMC Bioinformatics

    ProtSeqGen: a novel deep learning model for protein sequence design

    Qiang Gao, Zhijin Li, Yang Deng, Zhiwei Ji

    Discovered via OpenAlex

  611. bioRxiv (Cold Spring Harbor Laboratory)

    SynFit: Synergistic Contrastive Learning for Multi-Objective Protein Fitness Prediction and Optimization

    Tony Tu, Wei Huang, Ziang Li, Kerr Ding, Yang Yang, Yunan Luo

    Discovered via OpenAlex

  612. Scientific Reports

    NuConf: a rotamer library for DNA and RNA and its implementation in the protein design software MUMBO

    Marharyta O. Makarova, Martin Tillmann Stiebritz, Derman Basturk, Birthe Lemke, Beatrix Süß, Yves A. Muller

    Discovered via OpenAlex

  613. arXiv (Cornell University)

    Self-Improvement Imitation with Biologically Guided Search for Protein Design Under Oracle Budgets

    Ashima Khanna, Dominik G. Grimm

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 2. Model-based design · 2.5 Sampling-algorithms

  614. Figshare

    Additional file 1 of ProtSeqGen: a novel deep learning model for protein sequence design

    Qi Gao, Zhijin Li, Yang Deng, Zhiwei Ji

    Discovered via OpenAlex

  615. Annual Review of Biomedical Data Science

    Modeling the Language of Codons with Artificial Intelligence

    Claudèle Lemay-St-Denis, Rachel Kolodny

    Discovered via OpenAlex

  616. Proceedings of the National Academy of Sciences

    Navigating high-order protein fitness landscapes via deep learning on directed evolution trajectories

    Chengzhi Song, Liang Ma, Y Xu, Yingfan Xu, Qihan Zhang, Yuxi Liu, Chen Song, Yihan Lin

    Discovered via OpenAlex

  617. Bioresource Technology

    Generative AI-driven enzyme engineering unlocks sustainable valorization of broccoli waste into sulforaphane

    Hao Luo, Siyuan Guo, Yihong Bao, Shan Lu, Fengxia Lv, Ping Zhu

    Discovered via OpenAlex

  618. Journal of the American Chemical Society

    AI-Guided De Novo Design of a Caffeine-Induced Protein Dissociation System

    Tatsuki Nonomura, Brendan McKee, Anna Price, Mingguang Cui, Zaynah Yousuf, Faith Tran, Lian He, Tianlu Wang, Yubin Zhou

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 2. Model-based design · 2.1.1 trRosetta-based

  619. arXiv (Cornell University)

    SurfDesign: Effective Protein Design on Molecular Surfaces

    Fang Wu, Shuting Jin, Xiangru Tang, Mark Gerstein, Xiangxiang Zeng, Yejin Choi, Jure Leskovec, Jinbo Xu

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 4.7 Transformer-based · 4.Scaffold to Sequence

  620. Journal of Controlled Release

    CD40 agonistic-monovalent streptavidin fusion antibody for targeted neoantigen peptide delivery and potent cancer vaccination

    Dahee Jung, Xiaoying Cai, Ziye Wan, Elie Abi Khalil, Nawon Lee, Neal Thomas Ramseier, Qing Bao, Zongmin Zhao, Ying Chuan Hu, Seung‐Oe Lim, Seung Young Lee

    Discovered via OpenAlex

  621. Communications Biology

    Scaling antibody language models improves structure aware representation for antibody engineering

    Shengyuan Bai, Zijing Liu, Bin Feng, Jiying Zhang, Yu Li

    Discovered via OpenAlex

  622. arXiv (Cornell University)

    GeoCycler: Reward-Aligned 3D Diffusion for Constraint-Conditioned Cyclic Peptide Design

    Jingjie Zhang, Hanqun Cao, Haosen Shi, Mutian He, Yu Wang, Zijun Gao, Fang Wu, Xiaojun Yao, Chang‐Yu Hsieh, Sinno Jialin Pan, Pranam Chatterjee, Chunbin Gu, Pheng‐Ann Heng

  623. PLoS Computational Biology

    Scaffold-Lab: Critical evaluation and ranking of protein backbone generation methods in a unified framework

    Zhuoqi Zheng, Bo Zhang, Bozitao Zhong, Kexin Liu, Kexin Liu, J F Zhu, Jinyu Yu, Ting Wei, Haifeng Chen

    Discovered via OpenAlex

  624. arXiv (Cornell University)

    Contrastive Distribution Matching for Amortized Sequential Monte Carlo in Discrete Diffusion

    Jaihoon Kim, Taehoon Yoon, Prin Phunyaphibarn, Seungjun Kim, Morteza Mardani, Minhyuk Sung

    Discovered via OpenAlex

  625. Zenodo (CERN European Organization for Nuclear Research)

    AI-driven protein design to understand effector function within the Magnaporthe oryzae rice pathosystem

    Angus Bucknell, Hodasi Bright, Lauren S. Ryder, Vincent M. Were, Xia Yan, Adam R. Bentham, Nicholas J. Talbot

    Discovered via OpenAlex

  626. FEBS Journal

    Structural insights into tyrosine sulfation of CCR5 by human tyrosylprotein sulfotransferase‐1

    Shinnosuke Tanaka, Hirai Asano, Kota Toyoda, Toshiaki Nishiyori, Hidetaka Kojo, Kazuto Kiyomatsu, Katsuhisa Kurogi, Yoichi Sakakibara, Etsuko Nishimoto, Takamasa Teramoto, Yoshimitsu Kakuta

    Discovered via OpenAlex

  627. Bioorganic Chemistry

    β-Maltose-conjugated acetophenone thiosemicarbazones as multitarget inhibitors of diabetes- and Alzheimer's disease-related enzymes: Design, synthesis, and mechanistic evaluation

    Hoàng Thi Kim Van, Nguyễn Đình Thành

    Discovered via OpenAlex

  628. Combinatorial Chemistry & High Throughput Screening

    AI-Driven De novo Design of HDAC6/EZH2 Dual-target Peptide Inhibitors for Epigenetic Cancer Therapy

    Y X Zhang, Si Chen, ShiJie Gai, Xiaoli Zhi

    Discovered via OpenAlex

  629. Nature

    De novo design of miniproteins targeting GPCRs

    Edin Muratspahić, David Feldman, David E. Kim, Xiangli Qu, Ana-Maria Bratovianu, Paula Rivera-Sánchez, Jan Hendrik Voss, Emil Peter Thrane Hertz, Mads Gravers Jeppesen, Federica Dimitri, Kensuke Sakamoto, Amrita Nallathambi, Pia Peceli, Jianjun Cao, Brian P. Cary, Matthew J. Belousoff, Peter Keov, Phuc N. H. Trinh, Qingchao Chen, Yue Ren, Justyn Fine, Sudha Mishra, Annu Dalal, Shachie Sinha, Ramanuj Banerjee, Manisankar Ganguly, Karthik Varappalayam Karuppusamy, Isaac Sappington, Thomas Schlichthaerle, Jason Z. Zhang, Arvind Pillai, Brian Coventry, Ljubica Mihaljević, Magnus S. Bauer, Susana Vázquez Torres, Amir Motmaen, Gyu Rie Lee, Long Tran, Xinru Wang, Inna Goreshnik, Dionne K. Vafeados, Justin E. Svendsen, Parisa Hosseinzadeh, Nicolai Lindegaard, Matthäus Brandt, Yann Waltenspühl, Kristine Deibler, Lukas Deweid, Anja Bennett, Jendrik Schöppe, Tiantang Dong, Xiaoli Yan, Luke T. Oostdyk, William Cao, Lakshmi Anantharaman, Johan Juhl Weisser, Jesper F. Bastlund, Christoffer Bundgaard, Ayodeji A. Asuni, Justin G. English, Lance J. Stewart, Lauren Halloran, Jamie B. Spangler, André Lieber, Arun K. Shukla, Patrick Michael Sexton, Bryan L. Roth, Brian E. Krumm, Denise L. Wootten, Christopher G. Tate, Christoffer Norn, David A. Baker

  630. Nature Biotechnology

    AI-guided redesign of laboratory-evolved reverse transcriptases enhances prime editing

    Y. Allen Tao, Holt A. Sakai, Allen Yujie Jiang, Nicholas Andrew Krasnow, Vasilii Vaganov, Brian H. Shim, Zachary Barsdale, Smriti Pandey, Nouraiz Ahmed, Man Na, Ting-Wei Liao, Keyede Oye, Ana Cristian, Emily Zhang, J. Y. Xu, M. Bulcaen, David R. Liu

    Discovered via OpenAlex

  631. Frontiers in Bioinformatics

    Nature’s economy as blueprint: regional overlap & block-based algorithm for protein design

    Héctor Retana, Roberto Damián-Tentle, Luis A. Pineda, Myriam M. Altamirano‐Bustamante

    Discovered via OpenAlex

  632. Scientific Reports

    Design and classify innovative antimicrobial and dual- and multi-functional peptides using generative artificial intelligence

    Alexa Sowers, Jinge Wang, Gangqing Hu, Malcolm M. Q. Xing, Bingyun Li

    Discovered via OpenAlex

  633. The CRISPR Journal

    A Potent CRISPR-Cas12l Double-Strand Break Gene Editor

    Tomas Urbaitis, Laima Trinkuniene, Ieva Lenkaite, Monika Petrauskytė, Renatas Krasauskas, Migle Stitilyte, Modestas Sabaliauskas, Giedrius Sasnauskas, Giedrė Tamulaitienė, Joshua K. Young, Virginijus Šikšnys, Giedrius Gasiūnas

    Discovered via OpenAlex

  634. Journal of the American Chemical Society

    De Novo Design of Miniature and Efficient Metallo-Ketoreductases

    Y Xu, Yunhao Li, Hangwen Zheng, Elliot S. Delfosse, Gao Y, David A. Baker, Pengfei Ji

    Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.3 RoseTTAFold-based

  635. Nature

    Design of one-component quasisymmetric protein nanocages

    Sangmin Lee, David Chmielewski, Shunzhi Wang, Ryan D. Kibler, Jisu Shin, ANN CARR, Young‐Jun Park, David Veesler, David A. Baker

  636. Nature

    De novo design of quasisymmetric two-component protein cages

    Shunzhi Wang, Ying Xie, David Chmielewski, Connor Weidle, Tong Shu, Green Ahn, Ryan D. Kibler, Cindy Hernandez, Wei Chen, David Camilo Duran, ANN CARR, Asim K. Bera, Sangmin Lee, Justin A. Decarreau, Alex Kang, Evans Brackenbrough, Emily Joyce, Kejia Wu, Andrew J. Borst, Andrew Favor, Buwei Huang, Frank DiMaio, Liam J. Holt, David A. Baker

  637. bioRxiv (Cold Spring Harbor Laboratory)

    Control of Guanine Exchange Factor Activity Using De Novo Designed Protein Inhibitors

    Fabiola Vacca, Daniel J. Marston, Caitlin Harris, Pranav Kannan, Heman Burre, Jayani Christopher, Irina Dumbravanu, Mihai L. Azoitei

    Discovered via OpenAlex

  638. arXiv (Cornell University)

    EvoStruct: Bridging Evolutionary and Structural Priors for Antibody CDR Design via Protein Language Model Adaptation

    Mansoor Ahmed, Sujin Lee, Umar Khayaz, Murray Patterson

    Discovered via OpenAlex

  639. arXiv (Cornell University)

    AgForce Enables Antigen-conditioned Generative Antibody Design

    Mansoor Ahmed, Murray Patterson

    Discovered via OpenAlex

  640. Nature Communications

    Redesign of TALE proteins for DNA-templated assembly of protein fibers

    Robbert J. de Haas, Mark D. Langowski, Andrew J. Borst, Visakh V. S. Pillai, Gwendolyn E. Hoffmann, Martin Bongers, Matthias Mulder, Suna Cheng, Catherine Treichel, Elizabeth M. Leaf, Mengyu Wu, Eric M. Lynch, Justin M. Kollman, Francesco Simone Ruggeri, Carl Walkey, Renko J. de Vries, Neil P. King

  641. Bioresource Technology

    Multilevel cytochrome P450 engineering integrating protein language model-guided evolution enables de novo biosynthesis of amentoflavone in Escherichia coli

    Xuehui Dai, Jiangming Zhu, Zheyu Wu, Guangyi Wang, Yanchen Zhang, Chenfei Tian, Yuhong Ren, Haili Liu, Yong Wang

    Discovered via OpenAlex

  642. Nature Communications

    De novo design of a macrocycle-induced dimerization system for cellular control

    Stephanie Hanna, Patrick J. Salveson, Basile I. M. Wicky, Madison Kennedy, Derrick R. Hicks, Carolina Möller, Suna Cheng, Xinting Li, Mohamad H. Abedi, Brian Coventry, Meerit Y. Said, Asim K. Bera, Alex Kang, Barry L. Stoddard, David A. Baker

  643. bioRxiv (Cold Spring Harbor Laboratory)

    Extending structural surfaceomics to identify aberrant conformations of tumor surface proteins as potential immunotherapy targets

    Audrey Kishishita, Sabine Cismoski, Tianna Grant, Rucha Deo, Sanjana Prudhvi, Catherine Sue, Abhilash Barpanda, Clinton Yu, Sanjyot Vinayak Shenoy, Sarah Berman, Audrey G. Reeves, Haolong Li, Tianyi Liu, Akul Naik, Deeptarup Biswas, Fenglong Jiao, Yi He, MATTHEW J. HANCOCK, Radhika Dalal, Arthur O. Zalevsky, Michael R. Hoopmann, Chun Ye, Rosa Viner, Felix Yi-Chung Feng, Kamal Mandal, Robert L. Moritz, Ignacia Echeverria Riesco, Andrej Šali, James A. Wells, Sanjeeva Srivastava, Lan Huang, Arun P. Wiita

    Discovered via OpenAlex

  644. Biotechnology Advances

    Machine-guided design for bioengineering gene therapy vectors: Where are we and what lies ahead?

    Ana F. Rodrigues, Lucas Ferraz, Cátia Pesquita

    Discovered via OpenAlex

  645. bioRxiv (Cold Spring Harbor Laboratory)

    ConforFlux: Particle-Guided Trunk Repulsion for Diverse Protein Conformations

    Shosuke Suzuki, Toshiyuki Amagasa

    Discovered via OpenAlex

    Preprint source: bioRxiv: Bioinformatics

  646. bioRxiv (Cold Spring Harbor Laboratory)

    Genetic code expansion enables programmable covalent protein design

    Helena de Puig, Erkin Kuru, Michaël Moret, Allison Flores, Suneesh Karunakaran, Dinara Sayfullina, Subhrajit Rout, Carmen Escobedo‐Lucea, James J. Collins, George McDonald Church

    Discovered via OpenAlex

  647. arXiv (Cornell University)

    Ligand-Conditioned Discrete Diffusion for Protein Sequence-Structure Co-Design

    Chen Wei, Fanding Xu, Minghao Sun, Zhiyuan Liu, Lin Wang, Tianrui Jia, Yihang Zhou, Yang Zhang

    Discovered via OpenAlex

  648. Journal of Biotechnology

    Enhancement of glutaminase production through protein design and host strain modification in Bacillus amyloliquefaciens

    Dian Zou, Xiaoqi Ding, Pengfei Bao, Anying Ji, Zejing Mao, Xianliang Zheng, Xuetuan Wei

    Discovered via OpenAlex

  649. Al-Azhar Journal of Pharmaceutical Sciences/Al-Azhar Journal of Pharmaceutical Sciences

    DISCOVERY OF A NOVEL PHENYLAMINE-PURINE CHEMOTYPE AS A POTENTIAL EGFR INHIBITOR USING AN INTEGRATED AI-DRIVEN DRUG DESIGN PIPELINE

    Hany E. A. Ahmed, Abdullah Ashraf

    Discovered via OpenAlex

  650. Nature Machine Intelligence

    A generative artificial intelligence approach for peptide antibiotic optimization

    Marcelo D. T. Torres, Yimeng Zeng, Fangping Wan, Natalie Maus, Jacob R. Gardner, César de la Fuente‐Núñez

    Discovered via OpenAlex

  651. Journal of Assisted Reproduction and Genetics

    Novel anti-Mullerian hormone receptor 2 binding peptide prevents chemotherapy-related ovarian follicle loss in a mouse model

    Laura Detti, Michael C Mari, Michael P. Diamond, Michael D. Jochum, Feng Li, Laurie Jane McKenzie, Terri L. Woodard, Ghassan M. Saed

    Discovered via OpenAlex

  652. bioRxiv (Cold Spring Harbor Laboratory)

    Redesign selective protein binders using contrastive decoding

    Ziwei Xie, Jinbo Xu

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 4.7 Transformer-based · 4.Scaffold to Sequence

  653. Journal of Chemical Theory and Computation

    Statistical Thermodynamics Based Design Principles into the Temperature Induced Fold Switching of a Metamorphic Protein

    Sridip Parui, Anand Kumar Srivastava

    Discovered via OpenAlex

  654. Zenodo (CERN European Organization for Nuclear Research)

    End-to-end de novo design of Zn²⁺ metallohydrolase binders: an open-source canonical pipeline anchored by LigandMPNN's metal-coordination recovery

    Cheongwoo Han

    Discovered via OpenAlex

  655. ACS Omega

    Design of Multifunctional Bioactive Peptides for Potential Application in Food Packaging: A Machine-Learning-Integrated Optimization Framework

    Sree Nithish Reddy Gunapati, Sathish Kumar Gunaseelan, Arnab Dutta, Debirupa Mitra

    Discovered via OpenAlex

  656. Zenodo (CERN European Organization for Nuclear Research)

    A computational structural hypothesis for a TRPV4–ANO1 interface, and a stapled peptide designed to test it

    Elijah Shorette

    Discovered via OpenAlex

  657. Zenodo (CERN European Organization for Nuclear Research)

    Steering potentials, not bug fixes, eliminate catastrophic outliers in Boltz-2 cofold protein-ligand affinity prediction: a six-way protocol evaluation on zinc-hydroxamate MMP-1 inhibitors

    Cheongwoo Han

    Discovered via OpenAlex

  658. bioRxiv (Cold Spring Harbor Laboratory)

    Reverse-engineering amyloid strains with generative protein design

    Laxmikant G. Gadhe, Katerina Konstantoulea, Aneesh Mazumder, Jie Chen, Łukasz A. Joachimiak, Nikolaos N. Louros

    Discovered via OpenAlex

  659. Protein Science

    Robust and interpretable machine learning for affinity prioritization of designed protein interactors

    Yu‐Chen Lo, Keng‐Fu Chang, I-Hsuan Chu, Lu-Yi Chen, Kuen‐Phon Wu

    Discovered via OpenAlex

  660. bioRxiv (Cold Spring Harbor Laboratory)

    PTM-dCN: Latent Space Control for Post-Translational Modification–Aware Protein Design

    Sitao Zhang, Rui Qing, Tianming Huang, Edward Chen

    Discovered via OpenAlex

  661. arXiv (Cornell University)

    ProteinOPD: Towards Effective and Efficient Preference Alignment for Protein Design

    Yulin Zhang, He Cao, Zihao Jiang, Chenyi Zi, Zhipeng Zhou, Zijing Liu, Yu Li, Jia Li, Ziqi Gao

    Discovered via OpenAlex

  662. Biotechnology Advances

    Microbial biosynthesis of stilbenoids: A comprehensive review

    Shenmei Sun, Aoxing Zhang, Rui Zhang, Xiaonan Liu

    Discovered via OpenAlex

  663. arXiv (Cornell University)

    Modeling Atomic Conformational Ensembles of Proteins via Test-Time Supervision of Boltz-2 on Cryo-EM Density Maps

    Jay Shenoy, Miro A. Astore, Axel Levy, Frédéric Poitevin, Sonya M. Hanson, Gordon Wetzstein

    Discovered via OpenAlex

  664. PLANT PHYSIOLOGY

    Machine learning empowers precise discovery of disease-resistance genes in plants

    Zhenya Liu, X Wang, Shuo Cao, Tingyue Lei, Zhuyifu Chen, M Zhang, Zhongqi Liu, J M Li, Jianzhong Lu, Wenqi Ma, Bingxiong Su, Yanmei Peng, Yanshuai Xu, X Xu, Wei Zhang, Cong Tan, Chengjie Chen, Yiwen Wang, Yi Zhou

    Discovered via OpenAlex

  665. arXiv (Cornell University)

    Pushing Biomolecular Utility-Diversity Frontiers with Supergroup Relative Policy Optimization

    Xinwu Ye, He Cao, Hao Li, Bin Feng, Zijing Liu, Xiangru Tang, Yu Li, Shenghua Gao

    Discovered via OpenAlex

  666. arXiv (Cornell University)

    VibeProteinBench: An Evaluation Benchmark for Language-interfaced Vibe Protein Design

    Hyunjin Seo, Hongjoon Ahn, Jimin Park, Sungjun Han, Gyubok Lee, Soojung Yang, Cheng-Hao Liu, Joseph S. Brown, Chen, Leo, Gina El Nesr, Feyisayo Eweje, Sarah F. Gurev, Hyejin Lee, Junlang Liu, Zhihui Qi, Gyu Rie Lee, Sungsoo Ahn, Jamin Shin, Sangwon Jung

    Discovered via OpenAlex

  667. BioData Mining

    Generative models for antimicrobial peptide design: auto-encoders and beyond

    Lukas Beierle, Julian M. Hahnfeld, Alexander Goesmann, Reihaneh Mostolizadeh, Franz Cemič

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 1. Reviews · 1.3 Peptide design

  668. Figshare

    Additional file 2 of Generative models for antimicrobial peptide design: auto-encoders and beyond

    Lukas Beierle, Julian M. Hahnfeld, Alexander Goesmann, Reihaneh Mostolizadeh, Franz Cemič

    Discovered via OpenAlex

  669. arXiv (Cornell University)

    A putative, computationally stable structure of homotrimeric BP180/collagen XVII

    Congzhou M Sha

    Discovered via OpenAlex

  670. Communications Biology

    The latest AI breakthroughs in structural biology: protein binder design and conformational state prediction

    Luciano A. Abriata

    Discovered via OpenAlex

  671. Journal of Pharmacy & Pharmaceutical Sciences

    Artificial intelligence directed computational protein design: lessons from COVID-19 for pandemic-ready vaccines and antibody therapeutics

    Rahul Kaushik, Suyong Re

    Discovered via OpenAlex

  672. Experimental & Molecular Medicine

    De novo and scaffold-based design of GDF15 binders for cancer cachexia diagnostics and therapeutics

    Jinsook Ahn, Ryeongeun Cho, S. B. Kim, Dong Sun Lee, Ho Min Kim

    Discovered via OpenAlex

  673. bioRxiv (Cold Spring Harbor Laboratory)

    Benchmarking and behavioral characterization of LLM agents for protein design

    Jeonghyeon Kim, Philip A. Romero

    Discovered via OpenAlex

  674. bioRxiv (Cold Spring Harbor Laboratory)

    Structural bias in machine learning-guided peptide design

    Victor Daniel Aldas-Bulos, Fabien Plisson

    Discovered via OpenAlex

  675. bioRxiv (Cold Spring Harbor Laboratory)

    Zero-Shot Design of a Biobetter Cetuximab: Enhanced EGFR Affinity with Preserved Developability

    Iddo Nadav Weiner

    Discovered via OpenAlex

  676. Journal of Pharmacy and Pharmacology

    The peptide ACTY116 improved noradrenaline-induced cardiac hypertrophy and enhanced cardiac function by biasing receptor signaling toward the β-arrestin and against the Gαq protein

    Qiao Liu, Qingman Luo, Kecheng Tang, XueLing Chen, Xiaohui Li

    Discovered via OpenAlex

  677. arXiv (Cornell University)

    POETS: Uncertainty-Aware LLM Optimization via Compute-Efficient Policy Ensembles

    Nicolas Menet, Andreas Krause, Abbas Rahimi

    Discovered via OpenAlex

  678. bioRxiv (Cold Spring Harbor Laboratory)

    Computational design of membrane fusion proteins

    Masaharu Somiya, Sydney Funk, Dane Evan Zambrano, Takumi Yanase, Noriyuki Hamaoka, Alex Kang, Banumathi Sankaran, Asim K. Bera, Neil P. King

  679. ACS Sustainable Chemistry & Engineering

    Functional Catalysis by Heterochiral Peptides Designed to Mimic Carbonic Anhydrase for Carbon Dioxide Sequestration

    Kalpana Kumari, Kirthi Joshi, Naveen Kumar, Vipin Agarwal, Vibin Ramakrishnan

    Discovered via OpenAlex

  680. Zenodo (CERN European Organization for Nuclear Research)

    Glass Box Machine Learning to Aid the Design of Small Peptide Agonists from Very Sparse Data: The Example of Erythropoietin Analogues

    Barry Robson

    Discovered via OpenAlex

  681. Journal of Chemical Theory and Computation

    Distance-Restraint-Guided Diffusion Models for Sampling Protein Conformational Changes and Ligand Dissociation Pathways

    Tatsuki Hori, Yoshitaka Moriwaki, Ryuichiro Ishitani

    Discovered via OpenAlex

  682. Protein Science

    Limitations of the refolding pipeline for de novo protein design

    Kerlen T. Korbeld, Vsevolod Viliuga, Maximilian J. L. J. Fürst

    Discovered via OpenAlex

  683. Biotechnology and Bioengineering

    Protein Engineering of a Genetically Encodable Biosensor for Wastewater Detection of Profen NSAIDs

    Zoe Indiana Davis, Hao Tian, Ian R. Wheeldon, Sean R. Cutler, Timothy A. Whitehead

    Discovered via OpenAlex

  684. Research Square

    GYDE: A collaborative drug discovery platform for AI-powered protein design and engineering

    Kiran Mukhyala, Thomas A. Down, Mateusz Warowny, April Walker, Luigi D’Ascenzo, Donald Lee, Zhenru Zhou, Shengya Cao, Travis W. Bainbridge, John Nicoludus, Seth F. Harris

    Discovered via OpenAlex

  685. bioRxiv (Cold Spring Harbor Laboratory)

    Simple baselines rival protein language models in mutation-dense design of function tasks

    Itay Talpir, Sarel Jacob Fleishman

    Discovered via OpenAlex

  686. Life

    YoyoMut: Interactive Exploration of SARS-CoV-2 Mutation Fixation and Reversion Through Time

    Jana Penić, Tommaso Alfonsi, Giovanni Chillemi, Ingrid G. Prandi, Fabrizio Maggi, Anna Bernasconi, Daniele Focosi

    Discovered via OpenAlex

  687. bioRxiv (Cold Spring Harbor Laboratory)

    Fast and Ultra-Capable Protein Design: Advancing the Frontier Through Atomistic SE(3)-Equivariance with Genie 3

    Yi‐Cheng Lin, Minji Lee, Aakarsh Vermani, Ellena Jiang, Sebastiaan De Cooman, Matěj Špeťko, Mohammed AlQuraishi

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.2 Diffusion-based

  688. bioRxiv (Cold Spring Harbor Laboratory)

    Structure-derived synthetic sequences guide a protein language model toward metalloproteins

    Giulia Peteani, Gianmattia Sgueglia, Thomas Lemmin, Marco Chino

    Discovered via OpenAlex

  689. bioRxiv (Cold Spring Harbor Laboratory)

    DOMINO: Learning Domain Co-occurrence for Multidomain Protein Design

    Fengyuan Dai, Jin Su, Qingsong Tan, Huijiao Yang, Xibin Zhou, Fajie Yuan

    Discovered via OpenAlex

  690. arXiv (Cornell University)

    ProtDBench: A Unified Benchmark of Protein Binder Design and Evaluation

    Cong Liu, Milong Ren, Jiaqi Guan, Chengyue Gong, Jinyuan Sun, Xinshi Chen, Wenzhi Xiao

    Discovered via OpenAlex

  691. arXiv (Cornell University)

    A-CODE: Fully Atomic Protein Co-Design with Unified Multimodal Diffusion

    Chaoran Cheng, Jiaqi Guan, Milong Ren, Chengyue Gong, Cong Liu, Xinshi Chen, Ge Liu, Wenzhi Xiao

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.2 Diffusion-based

  692. Nature Chemistry

    Emergence of specific binding and catalysis from a designed generalist binding protein

    Yuda Chen, Sagar Bhattacharya, Lena Bergmann, G.J. Correy, Sophia K. Tan, Kaipeng Hou, J.T. Biel, Lei Lu, Ian J. Bakanas, Jason E. Gestwicki, Alexander N. Volkov, Ivan V. Korendovych, Nicholas F. Polizzi, James S. Fraser, William F. DeGrado

  693. Frontiers in Biophysics

    Linker peptide acts as an external mechanical clamp in a designed polyprotein

    Yue Wang, Bin Zheng, Peng Zheng

    Discovered via OpenAlex

  694. npj Drug Discovery.

    Deep learning-driven integrated pipeline for de novo design and synthesis of antimicrobial peptides

    Jiahui Liu, Yun Chen, Jian Tang, Xupu Xing, Jin‐Shun Lin, Juping Sun, Xin‐Hui Xing, Juan Li, Can Yang Zhang

    Discovered via OpenAlex

  695. Journal of Chemical Information and Modeling

    HighFold-MeD2: An Enhanced Boltz-2 Model for Accurate Structure Prediction of N-Methylated and d -Amino Acid Cyclic Peptides

    Zhigang Cao, Wentong Wang, Sen Cao, Chengyun Zhang, Jingjing Guo, Hongliang Duan

    Discovered via OpenAlex

  696. Zenodo (CERN European Organization for Nuclear Research)

    Cost-Aware Multi-Fidelity Bayesian Optimization with Runtime-Gated Cascading Tiers for Autonomous in silico Dermatology Discovery

    Cheongwoo Han

    Discovered via OpenAlex

  697. Carbohydrate Polymers

    Antibacterial and cell-instructive chitosan/NeoNectin hydrogels crosslinked via click chemistry enable osteogenic differentiation within ultra-soft matrices

    Daniel Cabrerizo‐Aguado, Federica Barbugian, Maria‐Pau Ginebra, Xinru Wang, David A. Baker, José María Manero, Jordi Guillem‐Marti

  698. bioRxiv (Cold Spring Harbor Laboratory)

    Integrin-independent Tie2 activation using de novo designed proteins

    Clara McCurdy, Yan Ting Zhao, Saurav Kumar, Brian Coventry, Anne Pink, Yaoyao Fu, Phillip Bohn, Siyu Zhu, Inna Goreshnik, Xinru Wang, Garrett Ruth, Rashmi Ravichandran, Julie Mathieu, Jonathan A. Cooper, DEBORAH HEYDENBURG FULLER, Ho Min Kim, Pipsa Saharinen, David A. Baker, Hannele Ruohola‐Baker

  699. Protein Science

    Stabilizing Plasmodium falciparum proteins for small molecule drug discovery

    Marius Amann, Tim Sträßer, Oliver Einsle, Stefan Günther

    Discovered via OpenAlex

  700. Journal of Chemical Information and Modeling

    Controlled Protein Design via Statistical Energy Functions: A Rossmann Fold Case Study

    Lu Zhang, Ce Wang, Shenglin Hu

    Discovered via OpenAlex

  701. Journal of the Arkansas Academy of Science

    Characterization of Stable Fibroblast Growth Factor 2 Using Consensus Protein Design

    Molly K. Walker

    Discovered via OpenAlex

  702. bioRxiv (Cold Spring Harbor Laboratory)

    Artificial intelligence aided design of peptides with custom secondary structure motifs and reduced amino acid alphabets

    Sean M Brown, Ashley B. Cohen, Scott N. Dean

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 4.3 LSTM-based · 4.Scaffold to Sequence

  703. arXiv (Cornell University)

    Co-Generative De Novo Functional Protein Design

    Xinrui Chen, Yizhen Luo, Siqi Fan, Zaiqing Nie

    Discovered via OpenAlex

  704. arXiv (Cornell University)

    Proteo-R1: Reasoning Foundation Models for De Novo Protein Design

    Fang Wu, Weihao Xuan, Heli Qi, Hanqun Cao, Heng-Jui Chang, Zeqi Zhou, Haokai Zhao, Ma Jian, Carl Ma, Yu‐Chi Cheng, Kuan Pang, Xiangru Tang, Zehong Wang, Guanlue Li, Hanchen Wang, Kejun Ying, Pan Lu, Chiho Im, Seungju Han, Peng Xia, Tinson Xu, Yinxi Li, Deyao Zhu, Pheng-Ann Heng, Naoto Yokoya, Masashi Sugiyama, Li Erran Li, Jure Leskovec, Yejin Choi

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.2 Diffusion-based

  705. Briefings in Bioinformatics

    InversePep: Diffusion-driven structure-based inverse folding for functional peptides

    Srinivas Kashyap Chilakamarri, Sneha Reddy Kasturi, Sai Pranav Reddy Yerrabandla, Sanjana Gogte, Vani Kondaparthi

    Discovered via OpenAlex

  706. Clinical Neuropathology

    Rapid polymer-based immunohistochemistry for intraoperative CNS tumor diagnosis: A validation study

    Julia Schuler, Sandra Baur, Federico Fusco, Felix Schicktanz, Benedikt Wiestler, Julian Canisius, Christian Mawrin, Denise Bernhardt, Arthur Wagner, Bernhard Meyer, Carolin Mogler, Claire Delbridge

    Discovered via OpenAlex

  707. Cell Reports Physical Science

    Open-source chemoinformatics platforms for multi-target structure-activity relationships

    J. Israel Espinoza‐Castañeda, César de la Fuente‐Núñez, José L. Medina‐Franco

    Discovered via OpenAlex

  708. American Journal of Respiratory and Critical Care Medicine

    A98-08 Artificial Intelligence-assisted Design of Novel Antimicrobial Peptides Against Mycobacterium Abscessus

    J L Gomez, U Hurtado, K Lopez, L. Victoria, Nataly Álvarez, Teresa Realpe, M S Gwin, A J Losier, C.J. Britto-Leon, M Pizarro Daniels, M. Campo Patino, J Robledo

    Discovered via OpenAlex

  709. Chemistry & Biodiversity

    Direct Conversion of Phytosterol to Testosterone via an Integrated Microbial–Enzymatic Strategy

    Shikui Song, Xirenayi Tuergong, Zihan Ding, Xinlin Dong, Lang Wang, Zhengding Su

    Discovered via OpenAlex

  710. Journal of Orthopaedic Translation

    From undruggable to degradable: A deep learning-enabled framework for precision orthopaedic protein degradation

    Lulu Zhang, Wang Yan, Dong Wang, Jianxiong Ma

    Discovered via OpenAlex

  711. Briefings in Bioinformatics

    Deep Prior Framework: integrating functional specificity with general plausibility for targeted protein evolution

    Senxin Zhang, Yining Qin, H Zhu, Fei‐Long Meng, Lei Jia, Xiaoqi Zheng

    Discovered via OpenAlex

  712. Protein Science

    Detection of protein symmetry and structural rearrangements using secondary structure elements

    Runfeng Lin, Sebastian E. Ahnert

    Discovered via OpenAlex

  713. bioRxiv (Cold Spring Harbor Laboratory)

    Predicting Supramolecular Self-Assembly of Peptide Structures with AlphaFold3

    Claire Sklar, Sunjoo Huh, Sabrina Chen, Jeffrey J. Gray

    Discovered via OpenAlex

  714. bioRxiv (Cold Spring Harbor Laboratory)

    A Conditional Variational Autoencoder with QSAR-Guided Surrogate-Weighted Fine-Tuning and Cross-Entropy Optimization for Targeted Antimicrobial Peptide Generation

    Ismael Castañón, Fangping Wan, César de la Fuente‐Núñez, Alessandro Pini, Chiara Falciani

    Discovered via OpenAlex

  715. Nature

    The past, present and future of de novo protein design

    Wei Yang, Shunzhi Wang, Gyu Rie Lee, Jason Z. Zhang, Alexis Courbet, David Juergens, Xinru Wang, Thomas Schlichthaerle, Mohamad H. Abedi, Robert J. Ragotte, Linna An, Indrek Kalvet, Samuel J. Pellock, Ljubica Mihaljević, Cameron Glasscock, Arvind Pillai, Adam J. Broerman, Nathan M. Ennist, Ella Haefner, Nora K. McNamara-Bordewick, Ian C. Haydon, Lance J. Stewart, Gaurav Bhardwaj, David A. Baker

  716. International Journal of Molecular Sciences

    Generative Protein Design: From Deep Learning Algorithms to Translational Applications

    Shaotong Luo, Bo Zhou

    Discovered via OpenAlex

  717. Nature Communications

    Generation of mixed-valency, modular multispecific antibodies using disulfide-linked Fc–FcγR complexes

    Miso Park, Kevin Ly, Bea Parcutela, Hyeran Choi, Carmina Ladra, Asaul Gonzalez, Yead Jewel, HyunJun Kang, Melissa Valerio, Aparna Krishnan, Timothy Walter Synold, Le Xuan Truong Nguyen, Guido Marcucci, John C. Williams

    Discovered via OpenAlex

  718. Pharmaceutics

    Integrative Peptide Drug Development: Chemical Engineering, AI-Driven Design, and Cell-Penetrating Peptides

    Yong Eun Jang, Minjun Kwon, Chan Woo Kwon, Seok Gi Kim, Ji Su Hwang, Nimisha Pradeep George, Seung Ryong Paik, Sampa Misra, Shaherin Basith, Seung Soo Sheen, Gwang Lee

    Discovered via OpenAlex

  719. PLoS Computational Biology

    MsgaBpred: A B-cell epitope predictor integrating AlphaFold3-predicted structures with multi-scale GCNs and pre-trained language model ESM-C

    Shanyue Wang, Aoyun Geng, Zhenjie Luo, Y Li, J H Xu, Yajie Meng, Leyi Wei, Quan Zou, Z D Zhang, Tao Wang, Feifei Cui

    Discovered via OpenAlex

  720. Frontiers in Microbiology

    Leveraging AI-driven predictors of enzyme pH optima to unravel microbial adaptation to environmental pH

    Peng Zhou, Zu-Xin Zhang, Xiaoyong Pan, Xinfeng Dai, Qiaoli Chen

    Discovered via OpenAlex

  721. bioRxiv (Cold Spring Harbor Laboratory)

    Discriminative Site-Directed Protein Engineering via Lightweight CASPE Platform

    Qiufeng Deng, Jie Qiao, Chuan Wang, Xinyue Ni, Yongyao Chang, Nan Zhao, Rui Zhai, Haiyang Cui, Xiujuan Li, Mingjie Jin

    Discovered via OpenAlex

  722. bioRxiv (Cold Spring Harbor Laboratory)

    Generative design of sequence specific DNA binding proteins

    Enisha Sehgal, Yuliya Politanska, Raktim Mitra, Paul T Kim, Nayim González-Rodríguez, Tushar Warrier, Andrew Kubaney, Akira Morishita, Riley N. Quijano, Jasper Butcher, Rohith Krishna, Robert J. Pecoraro, Brian J. Belmont, Nicole Roullier, Inna Goreshnik, Dionne K. Vafeados, Paul S. Kwon, Rachana Ramarao, Jussi Taipale, Cameron J. Glasscock, David A. Baker

    Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.3 RoseTTAFold-based

  723. bioRxiv (Cold Spring Harbor Laboratory)

    Designed Minibinders Rewire Receptor Signaling to Enable Functional Human Myogenic Reprogramming

    Riya Keshri, Zachary Foreman, Philip Barrett, Alexander J. Robinson, Gabriela Reyes, Ashish Phal, Aditya Krishnakumar, Ethan Narog, Melodie Chiu, Shruti Jain, Xinru Wang, David J. Lee, Marc Expòsit, Mohamad H. Abedi, Alec S.T. Smith, Sanjay R Srivatsan, Jay Shendure, Julie Mathieu, David L. Mack, David A. Baker, Hannele Ruohola‐Baker

  724. Journal of the American Chemical Society

    Orchestrating Metal-Hydride Reactivity in Engineered Metalloenzymes: Electronic and Electrostatic Determinants of the Reaction Mechanism

    Ritwika Chatterjee, Garima Jindal

    Discovered via OpenAlex

  725. Protein Science

    Family‐level specialization in protein domain insertion architectures

    Richard Dustin Schaeffer, Rui Guo, J D Zhang, Qian Cong, Nick V. Grishin

    Discovered via OpenAlex

  726. Zenodo (CERN European Organization for Nuclear Research)

    Development & Assessment of Assays Capable of Data Generation for Training and Benchmarking Models for PET Hydrolase Engineering

    Bijoy J. Desai, Aviv Spinner, David A. Estell, Chase Armer, Steffan B. Paul, Gina El Nesr, Neil Thomas, Evan Komp, Daniel Gutiérrez, Odeta Bondarevaite, Artem Kononenko, Andi Dhroso, Amanda Reider Apel, Peter J. Kelly

    Discovered via OpenAlex

  727. Nucleic Acids Research

    PythiaStudio: a one-stop protein engineering platform powered by Pythia model suite

    Jinyuan Sun, Kelun Shi, Han Li, 崔颖鹿, Luoyi Wang, Bian Wu

    Discovered via OpenAlex

  728. Antimicrobial Agents and Chemotherapy

    Synergistic antiviral effects of structure-guided peptides and a mutagenic base analog on SARS-CoV-2 replication

    Sergio Ortega-del Campo, Gregorio J. Fernandez-Ballester, Clara Blanes‐Mira, Víctor Guirado Osorio, Luis Díaz‐Martínez, Ana Isabel de Ávila, María Eugenia Soria, Brenda Martínez‐González, Francisco José Villena González, Josefa Gómez Maldonado, María Isabel Viciana Ramos, Encarnación Clavijo Frutos, Jesús L. Santos González, Ugo Bastolla, Celia Perales, Esteban Domingo, Enrique Viguera, Ana María Fernández‐Escamilla, Ana Grande-Pérez

    Discovered via OpenAlex

  729. Discover Applied Sciences

    Hybrid deep learning model (E2BNet) combining ESM2 and BiLSTM for 8-state protein secondary structure prediction

    Diganta Das Droba, Ayesha Banu, Miftiaz Inti Sami, Riad Hossain, Mahfuzulhoq Chowdhury

    Discovered via OpenAlex

  730. bioRxiv (Cold Spring Harbor Laboratory)

    Structure of a sparsely populated chimeric intermediate that facilitates fold-switching of a metamorphic protein

    Bodhisatwa Nandi, Ashok Sekhar

    Discovered via OpenAlex

  731. Zenodo (CERN European Organization for Nuclear Research)

    Ly-Algebra 5-Fold Supercell Protein Design: AlphaFold2 Validation of a Novel 20-Residue TrpCage Scaffold with 94.89 Mean pLDDT Across 5 Independent Models

    Chloe jane Tully

    Discovered via OpenAlex

  732. Zenodo (CERN European Organization for Nuclear Research)

    Ly-Algebra 59-Mer Supercell: De Novo Protein Design Achieving 97.39 Mean pLDDT and Ensemble Convergence sigma=0.53 Across Five AlphaFold2 Models, Computed on a $79 Budget Android Device via the TT-G41 Framework

    Chloe jane Tully

    Discovered via OpenAlex

  733. Biomedical Signal Processing and Control

    Integrated model for drug-target interaction prediction leveraging multiple protein language embeddings

    Shasha Tao, Jin Liu, Min Xiang, Xin Ma, Tongtong Huo, Xiaolin Ning

    Discovered via OpenAlex

  734. bioRxiv (Cold Spring Harbor Laboratory)

    Zero-shot design of a de novo metalloenzyme

    Gina El Nesr, Simon Dürr, Irimpan I. Mathews, Qi Wen Deng, Kewei Zhao, Ritimukta Sarangi, Ursula Röthlisberger, Fanny Sunden, Po‐Ssu Huang

    Discovered via OpenAlex

  735. bioRxiv (Cold Spring Harbor Laboratory)

    Additive baselines furnish no evidence for epistasis learning by MULTI-evolve

    Gian Marco Visani, Aayushi Verma, William S. DeWitt

    Discovered via OpenAlex

  736. Expert Systems with Applications

    From Heuristics to Deep Generative Models: A Critical Review of Protein Sequence Analysis Architectures for Clinical Decision Support Systems (CDSS)

    Faezeh Rahimzadeh, Leyli Mohammad Khanli, Pedram Salehpour, Faegheh Golabi

    Discovered via OpenAlex

  737. bioRxiv (Cold Spring Harbor Laboratory)

    An autonomous LLM-agent platform for computational binder design and conjugation-aware prioritization of antibody–drug conjugates

    Ganggang Liu, Mingjie He, Liang Sun, 成福仙, Yu Zhang

    Discovered via OpenAlex

  738. bioRxiv (Cold Spring Harbor Laboratory)

    Landscape-scale navigation unlocks antibody CDR structural logic for AI-guided rescue and therapeutic optimization

    Changju Chun, Byeong-Kwon Sohn, Heesoo Ki, Ji Hye Jo, Hyoung-Tae An, Jinseo Park, Jiyu Lee, Sooyeon Choi, J H Choi, Hyeyoung Cho, Seong Beom Lee, Booyoung Yu, Chae Young Lee, Ji Eun Kim, Yu-jin Ban, Young-Yoon Choi, Byoungsan Choi, 이홍원, Junho Chung, Minkyung Baek, Tae‐Young Yoon

    Discovered via OpenAlex

  739. PLoS Computational Biology

    Using experimental results of protein design to guide biomolecular energy-function development

    Hugh K. Haddox, Gabriel J. Rocklin, Francis C. Motta, Devin Strickland, Samer F. Halabiya, Cameron Cordray, Hahnbeom Park, Eric Klavins, David A. Baker, Frank DiMaio

  740. bioRxiv (Cold Spring Harbor Laboratory)

    De novo masking domains that gate TNF-family ligand assembly and activity

    Shota Kudo, Brian A. Kuhlman

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.3 RoseTTAFold-based

  741. bioRxiv (Cold Spring Harbor Laboratory)

    Protein inverse folding through joint modeling of surface and backbone geometry

    Yifan Hong, Yantong Cai, Yuhua Jiao, mingrui qi, Qilai Huang, Lei Sun

    Discovered via OpenAlex

  742. Plant Foods for Human Nutrition

    Advances in Alternative Protein Design: Nutritional Constraints, Sensory Limits, and Computational Solutions

    Karen Alejandra Tapia-Cervantes, Ericka Denice Herrera-Cardoso, Ma. Fabiola León‐Galván

    Discovered via OpenAlex

  743. bioRxiv (Cold Spring Harbor Laboratory)

    sdAbs-LLM: Generative Large Language Models For de novo Antibody Design and Agentic Evaluation

    Delower Hossain, Fuad Al Abir, Sixue Zhang, Jake Y. Chen

    Discovered via OpenAlex

  744. arXiv (Cornell University)

    Structure-guided molecular design with contrastive 3D protein-ligand learning

    Carles Navarro, Philipp Thölke, Gianni De Fabritiis

    Discovered via OpenAlex

  745. bioRxiv (Cold Spring Harbor Laboratory)

    Full-Atom MPNN Based Redesign of Plant Dehydrogenase Enables Thermostability Enhancement Without Loss of Stereoselectivity

    Bruno Di Geronimo, Jasmin Zuson, Ana Udženija, Andrea M. Chánique, Robert Kourist, Shina Caroline Lynn Kamerlin

    Discovered via OpenAlex

  746. Briefings in Bioinformatics

    Contemporary data-driven innovations in peptide-based therapeutic design

    Lipsa Priyadarsinee, Vyacheslav Kungurtsev, Vibhor Kumar, Bapi Chatterjee, Garikapati Narahari Sastry, N. Arul Murugan

    Discovered via OpenAlex

  747. Journal of Translational Medicine

    α-Helical peptides: design strategies and recent advances in biomedical applications

    Mengyuan Yin, Fei Ding, Luo Guanghua, Miaomei Yu

    Discovered via OpenAlex

  748. Current Opinion in Structural Biology

    Closing the loop: Experimentally validated methods in artificial intelligence–driven protein design

    Clayton W. Kosonocky, Sarah Alamdari, Kevin Yang, Ava P. Amini

  749. arXiv (Cornell University)

    RosettaSearch: Multi-Objective Inference-Time Search for Protein Sequence Design

    Meghana Kshirsagar, Allen Nie, Ching-An Cheng, Fanglei Xue, Rahul Dodhia, Juan Lavista Ferres, Kevin K. Yang, Frank DiMaio

  750. Bioorganic Chemistry

    Assessment of the antimicrobial properties of novel azopyrazolo[1,5-a]pyrimidine derivatives targeting DNA gyrase enzyme: design, synthesis, and molecular docking studies

    Rehab Sabour, Amel S. Younes, Shimaa Mohamed Abd El-Gilil, Mai M. El-Ashmony, Hager A. Bendary, Enas A. Taha, Fatma G. Abdulrahman

    Discovered via OpenAlex

  751. Zenodo (CERN European Organization for Nuclear Research)

    Lignin-IB-Peroxidase

    SINGHVI, PRIYANK, Hans Marx, Oliver Spadiut A

    Discovered via OpenAlex

  752. arXiv (Cornell University)

    ProtoCycle: Reflective Tool-Augmented Planning for Text-Guided Protein Design

    Yutang Ge, Guojiang Zhao, Sihang Li, Zheng Cheng, Zifeng Zhao, Hanchen Xia, Guolin Ke, Linfeng Zhang, Zhifeng Gao, Yuguang Wang

    Discovered via OpenAlex

  753. bioRxiv (Cold Spring Harbor Laboratory)

    The Synthetic Epitope Atlas: High-Throughput Design and Validation of De Novo Antibody-Antigen Complexes

    Nicholas Altieri, Joseph L. Harman, David Noble, Natasha Seelam Murakowska, Alexander Eng, Kerry L. McGowan, Davis Goodnight, Lucian DiPeso, Colleen Shikany, Emily Engelhart, Leah J. Homad, Miranda C. Lahman, Shyam Gandhi, Mackenzie Goodwin, Kendrick Herbst, Charles Lin, Margot McMurray, Juliana Barrett, Aditya A. Agarwal, James Harrang, Ryan Emerson, Randolph M. Lopez, David A. Younger, Adrian W. Lange

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 4.9 Diffusion-based · 4.Scaffold to Sequence

  754. Beni-Suef University Journal of Basic and Applied Sciences

    De novo design and evaluation of dual inhibitory peptide binders targeting MDMX-p53 and MDM2-p53 interactions

    Olanrewaju Ayodeji Durojaye, Sm Faysal Bellah, Henrietta Onyinye Uzoeto, Somtochukwu Precious Ezechukwu, Amarachukwu Vivian Arazu, Judith Nnedimkpa Ajima, Anthonia Ngozi Ngwu, Samuel Cosmas

    Discovered via OpenAlex

  755. Protein Science

    The double histone fold: Structure, functional implications across the tree of life and relevance to protein design

    Anna Ranaudo, Toshiko Miyake, Ugo Cosentino, Claudio Greco

    Discovered via OpenAlex

  756. bioRxiv (Cold Spring Harbor Laboratory)

    Integrating glycosylation in de novo protein design with ReGlyco Binder Design Filter

    Ojas Singh, Elisa Fadda

    Discovered via OpenAlex

  757. bioRxiv (Cold Spring Harbor Laboratory)

    Dynamic-Structure Redesign of Calmodulin Reveals Mechanistic Constraints on Ryr2 Regulation

    Vladimir Bogdanov, Svetlana B. Tikunova, Nicolas Fadell, Robyn T. Rebbeck, Melanie L. Aprahamian, Md Nure Alam Afsar, Aleksei Chekodanov, Daniel J. Blackwell, Björn C. Knollmann, Rǎzvan L. Cornea, Peter Michael Kekenes-Huskey, Steffen Lindert, Christopher N. Johnson, Sándor Györke, Jonathan P. Davis

    Discovered via OpenAlex

  758. ChemRxiv

    Computational Engineering of a Thermostable Enzyme for the Degradation of PET Through Manipulation of Disulfide Bonds

    Jackson Lieberman

    Discovered via OpenAlex

  759. Progress in Polymer Science

    Advances in computational and data-driven methodologies for accelerating antimicrobial peptide design and discovery

    Amal Jayawardena, Andrew Hung, Greg GuangHua Qiao, Elnaz Hajizadeh

    Discovered via OpenAlex

  760. ACS Omega

    Peptide Design for Targeting BTB Domain Homodimerization of BACH2: Complementary In Silico and In Vitro Approaches

    Efe Acar, Hüveyda Başağa, Emel Timuçin, Ahmet Can Timuçin

    Discovered via OpenAlex

  761. Nature Computational Science

    Enhancing success rates in therapeutic antibody design through generative models

    Discovered via OpenAlex

  762. STAR Protocols

    A protocol for single-sequence protein-RNA complex structure prediction using ProRNA3D-single

    Rahmatullah Roche, Sumit Tarafder, Debswapna Bhattacharya

    Discovered via OpenAlex

  763. ChemRxiv

    Predicting Ligand-Induced Conformational Selection: Co-Folding, Generative Docking, and the Pharmacophore Understanding Problem

    Jin Yeol Yang, Jong Gwan Jeong, Min Tae Kim, Sung Uk Cha, DAEHEE LEE

    Discovered via OpenAlex

  764. bioRxiv (Cold Spring Harbor Laboratory)

    Sampling antibody conformational ensembles with ABodyBuilder4-STEROIDS

    Fabian C. Spoendlin, Matteo Cagiada, King Ifashe, Odysseas Vavourakis, Charlotte Mary Deane

  765. Trends in biotechnology

    Deep learning-guided discovery and engineering of binding peptides for accelerated enzymatic degradation of polyethylene terephthalate

    Yidi Liu, Jianqiang Hu, Ke Tong, Xiaoyan Chen, Zhisheng Wei, Yihang Shen, Yueheng Niu, Jun Wan, Zhiyu Shen, Hanzhi Weng, Zihao Zhang, Yiming Zhao, Zhanzhi Liu, Jing Wu

    Discovered via OpenAlex

  766. Cell Biomaterials

    Artificial intelligence in antibiotic discovery: Applications, challenges, and future outlook

    Jing Bo Xu, Chen Li, Xiaoyu Wang, Anton Yariv Peleg, FUYI LI, Jiangning Song, César de la Fuente‐Núñez

    Discovered via OpenAlex

  767. bioRxiv (Cold Spring Harbor Laboratory)

    Generative design of intrinsically disordered proteins based on conditioned protein language models: Data is the limit

    Laure Carriere, Alexandre Huyghe, Mátyás Pajkos, Pau Bernadó, Juan Cortés

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 5.4 Transformer-based · 5.Function to Sequence

  768. Nature Biotechnology

    Artificial allosteric protein switches with machine-learning-designed receptors

    Zhong Guo, Oleh V. Smutok, Gyu Rie Lee, Zhenling Cui, Haocheng Qianzhu, Monika Kish, Cagla Ergun Ayva, Kejia Wu, Roxane Mutschler, Colin J. Jackson, Maria Micaela Fiorito, Andrew C. Warden, Oliver B. Smith, Alfredo Quijano‐Rubio, Thomas Huber, Jonathan J. Phillips, Gottfried Otting, Evgeny Katz, David A. Baker, Kirill A. Alexandrov

  769. Nature Computational Science

    DualGPT-AB: a dual-stage generative optimization framework for therapeutic antibody design

    Dongna Xie, Siyuan Chen, Xi Zeng, Dazhi Lu, Shaoqing Jiao, Shuyuan Xiao, Jiaming Liu, Jianye Hao, Hui Dai, Jiajie Peng

    Discovered via OpenAlex

  770. bioRxiv (Cold Spring Harbor Laboratory)

    A Hybrid Physics-Deep Learning Framework for Combinatorial De Novo Design of Small-Molecule Binding Proteins

    Connor V. Galvin, Amy B. Guo, Maple N. Chen, Isabella Alfonso, Dominic Waldo Grisingher, Simon Kretschmer, Divya Kranthi, Mark J. S. Kelly, Tanja Kortemme

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 4.5 GNN-based · 4.Scaffold to Sequence

  771. Journal of Agricultural and Food Chemistry

    A T-Cell Epitope Tandem Peptide Designed from Two Major Allergens of Crassostrea angulata Shows Potential for Inducing Dual Immune Tolerance

    Yi Gu, Fei Huan, Shuai Gao, Meng Liu, Lingna Ni, Ming-Xuan Wu, Xin-Yi Huang, Yang Yang, Dong Lai, Guang‐Ming Liu

    Discovered via OpenAlex

  772. arXiv (Cornell University)

    BOAT: Navigating the Sea of In Silico Predictors for Antibody Design via Multi-Objective Bayesian Optimization

    Jackie Rao, Ferran Gonzalez Hernandez, Leon Gerard, Alexandra Gessner

    Discovered via OpenAlex

  773. UNC Libraries

    Perturbing the energy landscape for improved packing during computational protein design

    Samer F. Halabiya, Jermel R. Griffin, Hugh K. Haddox, Devin Strickland, David F. Thieker, Thomas Szyperski, Jack B. Maguire, Brian Coventry, Surya V. S. R. K. Pulavarti, Matthew C. Cummins, Brian A. Kuhlman, David A. Baker, Eric Klavins, Frank DiMaio

  774. CryoAtom2: inverse folding-inspired deep learning enables accurate model building of protein-nucleic acid complexes in cryo-EM

    Baoquan Su, Lingfan Zhu, Wenfei Li, Wenkai Wang, Jiahui Liang, K. B. Zhao, Zhenling Peng, Jianyi Yang

    Discovered via OpenAlex

  775. Bioinformatics

    From atoms to fragments: a coarse representation for efficient and functional protein design

    Leonardo V. Castorina, Christopher W. Wood, Kartic Subr

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 3. Function to Scaffold · 3.4 Diffusion-based

  776. Langmuir

    Peptide–Lipid Nanoparticles Enhance Cell Transfection Efficiency

    Yuzhi Ye, Hailiang Hu, Lei Yue, Rongxin Su, Wei Qi, Yuefei Wang

    Discovered via OpenAlex

  777. arXiv (Cornell University)

    Pareto-Optimal Offline Reinforcement Learning via Smooth Tchebycheff Scalarization

    Aadyot Bhatnagar, Peter Mørch Groth, Sebastian Ibarraran, Ali Madani

    Discovered via OpenAlex

  778. Briefings in Bioinformatics

    Comprehensive evaluation of artificial intelligence-empowered approaches for protein–aptamer complex prediction

    Jiani Zhao, Kha Tram, Hongbin Yan, Yifeng Li

    Discovered via OpenAlex

  779. Current Opinion in Structural Biology

    Steering generative models for protein design: Aligning and conditioning strategies

    Filippo Stocco, Michele Garibbo, Noelia Ferruz

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 1. Reviews · 1.1 De novo protein design

  780. Toxicology and Industrial Health

    Integrative computational elucidation of molecular mechanisms and multi-target interactions in paraquat-induced pulmonary fibrosis

    Guiyan Du, Shengyao Tang, Tian Shi, Guosheng Liu, Xia Huang, Jian Hua Chang

    Discovered via OpenAlex

  781. Frontiers in Bioinformatics

    AI-driven discovery in protein science for immunology and infectious disease research

    Mohamed Helmy, Fatma S. El- Shafei, Diogo Vieira da Silva Pellegrina, Lingling Jin, Amr Alhossary, Heather L. Wilson, Tamer A. Mansour, Kumar Selvarajoo

    Discovered via OpenAlex

  782. Theoretical and Natural Science

    AI-Driven Prediction of Enzyme Structure and Function and Its Applications

    Xiuquan Zhong

    Discovered via OpenAlex

  783. arXiv (Cornell University)

    Entangled happily ever after: Wedding reception seating mapped to classical and quantum optimizers

    Karie A. Nicholas Vikram Khipple Mulligan, Vikram Khipple Mulligan

    Discovered via OpenAlex

  784. Orvosi Hetilap

    Új klonalitásvizsgálat a T-sejt-receptor béta-láncának konstans-1 és -2 régiójára specifikus antitestek használatával T-sejtes lymphoproliferatiókban

    Barbara Forró, Livia Vida, László Kereskai, Ágnes Lacza, Pál Jáksó

    Discovered via OpenAlex

  785. bioRxiv (Cold Spring Harbor Laboratory)

    Generative design of intrinsically disordered protein regions with IDiom

    Jason Liu, Sebastian Ibarraran, Frank Hu, Abigail Park, Alexander R. Dunn, Grant M. Rotskoff

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 5.4 Transformer-based · 5.Function to Sequence

  786. Biochemistry

    AI-Designed Peptides as Tools for Biochemistry

    Lauren Hong, Sophia Vincoff, Pranam Chatterjee

  787. arXiv (Cornell University)

    Biologically-Grounded Multi-Encoder Architectures as Developability Oracles for Antibody Design

    Simon Crouzet

    Discovered via OpenAlex

  788. Zenodo (CERN European Organization for Nuclear Research)

    Thetazymes: Molecular Catalysts for Semantic Transitions Enzyme Design from Cost Minimization Applied to Meaning

    Washburn

    Discovered via OpenAlex

  789. bioRxiv (Cold Spring Harbor Laboratory)

    Modification-aware AI enables terminal chemical modifications for peptide design and discovers potent antimicrobials

    Jin Xu, Marcelo D. T. Torres, Chen Li, Jian Li, Fuyi Li, Jiangning Song, César de la Fuente‐Núñez

    Discovered via OpenAlex

  790. Proceedings of the National Academy of Sciences

    Negative design enables cell-free expression and folding of designed transmembrane β-barrels

    Giacomo Pedrelli, Marvelous Chikerema, Andrei S. Sokolovskii, Tamás Lázár, Alexander V. Shkumatov, Alexander N. Volkov, Anastassia Andreevna Vorobieva

    Discovered via OpenAlex

  791. Scientia Sinica Chimica

    AI protein design: constructing superstable proteins via maximized hydrogen bonding

    文科 张

    Discovered via OpenAlex

  792. Chemical Engineering Journal Advances

    AI-guided engineering of FAD-glucose dehydrogenase for enhanced processability and functional performance

    SuJin Lee, Soo Hong Min, Yea-Ju Han, Hyun-Jo Shim, Seong-Ryung Go, Kwang‐Hyun Park, Hahnbeom Park, Eui‐Jeon Woo

    Discovered via OpenAlex

  793. Probiotics and Antimicrobial Proteins

    Marine Antimicrobial Peptides: From Ocean Biodiversity to Genome Mining, Multi-Omics Discovery, and Biotechnological Innovation in the Battle Against Antimicrobial Resistance

    Hassan Aboul-Ella, Heba Aboul-Ella, Mahanama De Zoysa

    Discovered via OpenAlex

  794. Journal of Chemical Information and Modeling

    Controllable Protein Design by Prefix-Tuning Protein Language Models

    Jiawei Luo, Jiahao Li, Xianliang Liu, Yang Zhang, Qingcai Chen, Junjie Chen

    Discovered via OpenAlex

  795. arXiv (Cornell University)

    General Multimodal Protein Design Enables DNA-Encoding of Chemistry

    Jarrid Rector-Brooks, Théophile Lambert, Marta Skreta, Daniel Roth, Yueming Long, Zi-Qi Li, Xi Zhang, Miruna Cretu, Francesca-Zhoufan Li, Tanvi Ganapathy, Emily Jin, Avishek Joey Bose, Jason Yang, Kirill Neklyudov, Yoshua Bengio, Alexander Tong, Frances H. Arnold, Chenghao Liu

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.2 Diffusion-based

  796. bioRxiv (Cold Spring Harbor Laboratory)

    A Rapid and Universal Pipeline for High-Resolution GPCR Structure Determination through In Silico Construct Optimization and de novo Protein Design

    Asato Kojima, Kouki Kawakami, Naoya Kobayashi, Kazuhiro Kobayashi, Toshiki E. Matsui, Kohei Uemoto, Yuzhong Gu, Masahiro Fukuda, Hideaki E. KATO

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 2. Model-based design · 2.1.1 trRosetta-based

  797. Zenodo (CERN European Organization for Nuclear Research)

    Jensen NHC-Scaffolded Ambient Nitrogenase: A De Novo Protein-Engineered Catalyst That Achieves Room-Temperature, Atmospheric-Pressure N₂ Fixation Superior to Both Biology and Haber-Bosch

    Brent Allen Jensen

    Discovered via OpenAlex

  798. Biomacromolecules

    Progress in Self-Assembled Extracellular Matrix Structural Protein Mimetic Peptides: From Rational Design and Assembly Pathways to Biomedical Applications

    Linyan Yao, Jianxi Xiao

    Discovered via OpenAlex

  799. ACS Applied Materials & Interfaces

    BB-EIT: A Generalized Prediction Model for Protein Adsorption on Polymer Brushes Using Augmented Chemical Embeddings

    Shiwei Su, Nobuyuki Tanaka, Yoshitaka Ushiku, Koichi Takahashi

    Discovered via OpenAlex

  800. Zenodo (CERN European Organization for Nuclear Research)

    A Unified Substrate-Mediated Framework for Protein Function

    Nicolas Antony Brown

    Discovered via OpenAlex

  801. Journal of Chemical Information and Modeling

    High-PepBinder: A pLM-Guided Latent Diffusion Framework for Affinity-Aware Target-Specific Peptide Design

    Qingyi Mao, Silong Zhai, Sen Cao, Renjie Zhu, Wen Xu, Chengyun Zhang, Zhu Ning, Jingjing Guo, Hongliang Duan

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 5.12 Diffusion-based · 5.Function to Sequence

  802. Journal of Chemical Information and Modeling

    Leveraging Auxiliary Potentials in RFDiffusion for the Design of NA-Binding Proteins

    Elizaveta Geraseva, Grigoriy V. Bokov, Vladimir Polovnikov, Andrey V. Golovin

    Discovered via OpenAlex

  803. Bioinformatics

    Protein FID: improved evaluation of protein structure generative models

    Felix Faltings, Hannes Stark, Tommi Jaakkola, Regina Barzilay

  804. Frontiers in Microbiology

    Protein design, generative AI and biological security

    Maximilian Brackmann, Sophie Reiners, Masja Hoogendoorn, Michel Moser

    Discovered via OpenAlex

  805. bioRxiv (Cold Spring Harbor Laboratory)

    CROWN: Curated Repository Of Well-resolved Non-covalent interactions

    Robin Poelmans, Wout Van Eynde, Bence Bruncsics, Bruncsics Balint, Ádám Arany, Yves Moreau, Arnout R. D. Voet

    Discovered via OpenAlex

  806. ChemBioChem

    Integrating the Biosynthesis and Genetic Encoding of Noncanonical Amino Acids for Enzyme Design and Catalysis

    Yuhui Sheng, Zhi Zhou

    Discovered via OpenAlex

  807. ChemBioChem

    Exploring PadR Proteins for Artificial Enzyme Design

    Bart Brouwer, A.M.W.H. Thunnissen, Henriëtte J. Rozeboom, Gérard Roelfes

    Discovered via OpenAlex

  808. Cell Death

    Structure-based design of p62-derived peptides that inhibit autophagy-associated readouts and enhance chemotherapy response in breast cancer cells

    Fatemeh Mokhles, Shiva Azimee, Marco Cordani, Marveh Rahmati, Najaf Allahyari Fard, Mojgan Djavaheri‐Mergny, Mohammad Amin Moosavi

    Discovered via OpenAlex

  809. Microbial Biotechnology

    Transglycosylation Capabilities of Wild‐Type α‐ l ‐Fucosidase iso1 from Paenibacillus thiaminolyticus and Its Engineered Mutants: Preparation of Fucosylated Oligosaccharides

    Patricie Vodičková, Lucie Klimešová, Pavlína Nekvasilová, Lucie Petrásková, Helena Pelantová, Terézia Kovaĺová, Petra Lipovová, Pavla Bojarová, Eva Benešová

    Discovered via OpenAlex

  810. Zenodo (CERN European Organization for Nuclear Research)

    Deep Learning-Based Prediction of Protein Structure for Novel Antimicrobial Peptide Design

    Schuster F, Renaud J, Todorova R

    Discovered via OpenAlex

  811. bioRxiv (Cold Spring Harbor Laboratory)

    Explainable protein-protein binding affinity prediction via fine-tuning protein language models

    Harshit Singh, RAJEEV KUMAR SINGH, Satya Pratik Srivastava, Suryavedha Pradhan, Rohan Gorantla

    Discovered via OpenAlex

  812. Microbial Biotechnology

    Deep Learning‐Enabled Engineering of a Hyper‐Stable and Soluble MPB70 ‐83 Antigen for Sensitive Bovine Tuberculosis Surveillance

    Wen‐Hao Wang, Jia‐Zhen Ge, Ying‐Ying Xie, Guo‐Dong Song, Yijian Liu, Yin-Juan Song, Ren‐ge Li, RC Li, Z Wang, Xin‐Miao Liu, Shuang‐Shuang Guo, Jie Li, Shengli Chen, Na Li, Fuying Zheng, Yuefeng Chu

    Discovered via OpenAlex

  813. Journal of the American Chemical Society

    Biosynthetic Lanthanide-Luminescent Mini-Proteins Using Genetic Code Expansion

    Edan Habel, Haocheng Qianzhu, Elwy H. Abdelkader, Nathan Paul, Gottfried Otting, Thomas Huber

    Discovered via OpenAlex

  814. Proceedings of the National Academy of Sciences

    Descent from a common ancestor restricts exploration of protein sequence space

    Lada H. Isakova, Elizaveta Streltsova, Olga Bochkareva, Peter K. Vlasov, Fyodor A. Kondrashov

    Discovered via OpenAlex

  815. bioRxiv (Cold Spring Harbor Laboratory)

    Decoupling Topology from Geometry: Detecting Large-Scale Conformational Changes via Conformational Scanning

    Runfeng Lin, Sebastian E. Ahnert

    Discovered via OpenAlex

  816. arXiv (Cornell University)

    Latent-Y: A Lab-Validated Autonomous Agent for De Novo Drug Design

    Latent Labs Team, Sebastian M. Schmon, Daniella Pretorius, Simon V. Mathis, Rebecca Bartke-Croughan, Aishaini Puvanendran, James Vuckovic, Henry Kenlay, Mária Vlachynská, Alex Bridgland, Ivan Grishin, S. Over, David Li, Bridget Li, Jonathan Crabbé, Agrin Hilmkil, Alexander W. R. Nelson, David Yuan, Annette Obika, Simon A. A. Kohl

    Discovered via OpenAlex

  817. arXiv (Cornell University)

    Scaling Atomistic Protein Binder Design with Generative Pretraining and Test-Time Compute

    Kieran Didi, Zuobai Zhang, Guoqing Zhou, Danny Reidenbach, Zhonglin Cao, Sooyoung Cha, Tomas Geffner, Christian Dallago, Jian Tang, Michael M. Bronstein, Martin Steinegger, Emine Küçükbenli, Arash Vahdat, Karsten Kreis

    Discovered via OpenAlex

  818. bioRxiv (Cold Spring Harbor Laboratory)

    Symmetric Self-play Online Preference Optimization for Protein Inverse Folding

    Wenwu Zeng, Xiaodong Li, H. Xuanpengfan Zou, Yutao Dou, Xiongjun Zhao, Shaoliang Peng

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 3. Function to Scaffold · 3.5 RL-based

  819. Nature Communications

    Deep homology and design of proteasome chaperone proteins in Candidozyma auris

    Jackson R. Rapala, Mohammad A. Siddiq, Patricia Jean Wittkopp, Matthew J. O’Meara, Teresa R. O’Meara

    Discovered via OpenAlex

  820. The Canadian Journal of Chemical Engineering

    Artificial intelligence in enzyme catalysis: Emerging trends and applications in biocatalyst engineering

    Misael Bessa Sales, Francisco Izaias da Silva Aires, Paulo Gonçalves de Sousa, Calebe da Rocha Silva, Emanuel Lino Rodrigues, Maria Cristiane Martins de Souza, José C. S. dos Santos

    Discovered via OpenAlex

  821. Research consortium archive.

    Artificial Intelligence and Bioinformatics for Predicting Protein Structure, Function, and Molecular Interactions

    Hafsa Hafeez, Ali Hassan, Fatima Ali, Muhammad Farman

    Discovered via OpenAlex

  822. Advanced Healthcare Materials

    Dual‐Peptide Nanoplatform: Mesoporous Silica Nanoparticles Functionalized With a Cell‐Penetrating Peptide and Loaded With Rationally Designed Antimicrobial Peptides for Tuberculosis Therapy

    Christian Shleider Carnero Canales, Cesar Augusto Roque‐Borda, Ana Carolina Cerqueira Negri, Oswaldo Julio Ramirez Delgado, Letícia Oliveira Catarin Nunes, Flávia Aparecida Resende, Hernane da Silva Barud, Norival Alves Santos‐Filho, Saulo Santesso Garrido, Karen Cristina Oliveira, Alexandra Ivo de Medeiros, Rafael Miguel Sábio, Fernando Rogerio Pavan

    Discovered via OpenAlex

  823. Nature Communications

    Small-molecule binding and sensing with a designed protein family

    Gyu Rie Lee, Samuel J. Pellock, Christoffer Norn, Doug Tischer, Justas Dauparas, Ivan V. Anishchenko, Jaron A. M. Mercer, Alex Kang, Asim K. Bera, Hannah Nguyen, Evans Brackenbrough, Banumathi Sankaran, Inna Goreshnik, Dionne K. Vafeados, Nicole Roullier, Hannah L. Han, Brian Coventry, Hugh K. Haddox, David R. Liu, Andy Hsien-Wei Yeh, David A. Baker

    Curated by Papers for Protein Design Using Deep Learning · 4.5 GNN-based · 4.Scaffold to Sequence

  824. Journal of Molecular Structure

    Triazole-centered bis-oxadiazole hybrids as high-affinity inhibitors of key diabetic enzymes: Design rationale, synthesis and computational validation

    Abdulmajeed Abdullah Alayyaf, Shoaib Ahmed Khan, Tayyiaba Iqbal, Wajid Ur Rehman, Kasim Sakran Abass, Mohammad Shahidul Islam, Hamdy Kashtoh

    Discovered via OpenAlex

  825. Chemistry

    Protein Engineering and Immobilization of Imine Reductases for Pharmaceutical Synthesis: Recent Advances and Applications

    Nevena Kaličanin, Nikolina Popović Kokar, Milica M. Spasojevic Savkovic, Anja Stošić, Olivera Prodanović, Nevena Surudzic, Radivoje Prodanović

    Discovered via OpenAlex

  826. npj Systems Biology and Applications

    KinForm: kinetics-informed feature optimised representation models for enzyme kcat and KM prediction

    Saleh Alwer, Ronan M. T. Fleming

    Discovered via OpenAlex

  827. bioRxiv (Cold Spring Harbor Laboratory)

    GYDE: A collaborative drug discovery platform for AI-powered protein design and engineering

    Thomas A. Down, Mateusz Warowny, April Walker, Luigi D’Ascenzo, Donald Lee, Zhenru Zhou, Shengya Cao, Travis W. Bainbridge, John M. Nicoludis, Seth F. Harris, Kiran Mukhyala

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 7. Other tasks · 7.4 Framework

  828. arXiv (Cornell University)

    Generative Modeling in Protein Design: Neural Representations, Conditional Generation, and Evaluation Standards

    Senura Hansaja Wanasekara, Minh-Duong Nguyen, Xiaochen Liu, Nguyen Tran, Ken‐Tye Yong

    Discovered via OpenAlex

  829. ACS Applied Materials & Interfaces

    Rational Design of Peptide-Metal Coassemblies for Biomimetic Laccase: Integrating Computation and Experiment

    Lu Yu, Qian-Qian Jiang, Yue-Hong Pang, Xiaofang Shen

    Discovered via OpenAlex

  830. Cell Reports Methods

    Development of motif-specific monoclonal antibodies for global protein citrullination detection with minimal cross-reactivity to homocitrullination

    Sophia Laposchan, Erik Riedel, Andrew Flatley, Selina Pasquero, Regina Feederle, Chien‐Yun Lee

    Discovered via OpenAlex

  831. Scientific Reports

    Exploring the limits of pre-trained embeddings in machine-guided protein design: a case study on predicting AAV vector viability

    Ana F. Rodrigues, Lucas Ferraz, Laura Balbi, Pedro Giesteira Cotovio, Cátia Pesquita

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 7. Other tasks · 7.1 Effects of mutation & Fitness Landscape

  832. Molecular Plant

    AI-driven protein engineering: A new paradigm for plant trait design

    Ran Fu, Shan Jiang, Tong Wu, Can Yin, Jun Yan, Xiangfeng Wang

    Discovered via OpenAlex

  833. Protein Science

    ProteinMCP : An agentic AI framework for autonomous protein engineering

    Xiaopeng Xu, Chenjie Feng, Chao Zha, Wenjia He, Maolin He, Bin Xiao, X.-J. Gao

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 7. Other tasks · 7.4 Framework

  834. bioRxiv (Cold Spring Harbor Laboratory)

    AI-guided design of candidate BMPR1A-binding peptides for cartilage regeneration: a multi-tool computational benchmarking study

    Asım Ahmadov, Olga Ahmadov

    Discovered via OpenAlex

  835. Current Biotechnology

    Discovering the Correlation between Theoretical and Experimental Binding Data for the HLA-A*0201 Molecule Using an Inverse Folding Approach

    Satarudra Prakash Singh, Bhartendu Nath Mishra

    Discovered via OpenAlex

  836. Nano Letters

    Polymerized Short Sequences as a Template for Protein Folding and Evolution

    Tianyi Jin, Jacob Sass, Wenhao Gao, Aiden A. Hurst, Connor W. Coley, Alfredo Alexander‐Katz

    Discovered via OpenAlex

  837. bioRxiv (Cold Spring Harbor Laboratory)

    “Visualize, Explore, and Select”: A Protein Language Model-based Approach Enabling Navigation of Protein Sequence Space for Enzyme Discovery and Mining

    Felix Moorhoff, David Medina-Ortiz, Alicja Kotnis, Ahmed Hassanin, Mehdi D. Davari

    Discovered via OpenAlex

  838. Matter

    VibeGen: Agentic end-to-end de novo protein design for tailored dynamics using a language diffusion model

    Bo Ni, Markus J. Buehler

    Discovered via OpenAlex

  839. Protein Science

    SegDesign : A modular framework for controllable protein segment engineering

    Chenjie Feng, Junbo Yin, Chao Zha, Mohammed Saif, Xiaopeng Xu, Xin Gao, Wenjia He

    Discovered via OpenAlex

  840. arXiv (Cornell University)

    ZeroFold: Protein-RNA Binding Affinity Predictions from Pre-Structural Embeddings

    Josef Hanke, Sebastian Pujalte Ojeda, S. J. Zhang, Werngard Czechtizky, Leonardo De Maria, Michele Vendruscolo

    Discovered via OpenAlex

  841. International Journal of Cosmetic Science

    Bio‐active designed peptide for hair keratin strengthening

    Chan‐Su Rha, Byeong Gyu In, Kilsun Myoung, Chaeyeon Song, Eun-Soo Lee, Heung Soo Baek, Won Seok Park

    Discovered via OpenAlex

  842. International Journal of Biological Macromolecules

    Computational de novo design of an α-helical peptide targeting LIMD2 suppresses breast cancer cell proliferation

    Qiuyan Huang, Yushuai Yu, Kai Huang, Zhengwen Zhu, Xinglong Wang, Chuangui Song

    Discovered via OpenAlex

  843. Zenodo (CERN European Organization for Nuclear Research)

    MIRADOR: Manifold of Immune Receptors And Drift-Optimized Responses : Geometry-First Co-Embedding for Vaccine and Antibody Design

    Bee Rosa Davis

    Discovered via OpenAlex

  844. Future Foods

    PepBERT: Lightweight language models for bioactive peptide representation

    Zhenjiao Du, Doina Caragea, Xiaolong Guo, Yonghui Li

    Discovered via OpenAlex

  845. Bioinformatics

    Evaluating deep learning based structure prediction methods on antibody–antigen complexes

    Samuel Fromm, Marko Ludaic, Arne Elofsson

    Discovered via OpenAlex

  846. Bioresource Technology

    Engineering a hybrid chemical-biological system for efficient de novo taurine production via computational enzyme design and pathway engineering

    Lingcong Li, Congcong LI, Yanan Chen, Zhoutong Sun, Ge Qu, Liang Wei, Jun O. Liu

    Discovered via OpenAlex

  847. ACS Catalysis

    Design, Optimization and Characterization of a de novo Gold Hydroaminase

    Elinor Morris, Boris V. Lozhkin, Jan Uhrhan, Indrek Kalvet, Sophie Basler, Roman Peter Jakob, David A. Baker, Thomas R. Ward

  848. Nature Communications

    Functional protein design and enhancement with ontology reinforcement iteration

    Bing He, Chenchen Qin, Yu Shan Zhao, Long-Kai Huang, Zihan Wu, Fang Wang, Fandi Wu, Fan Yang, Jianhua Yao

    Discovered via OpenAlex

  849. bioRxiv (Cold Spring Harbor Laboratory)

    ST-PARM: Pareto-Complete Inference-Time Alignment for Multi-Objective Protein Design

    Rujie Yin, Yang Shen

    Discovered via OpenAlex

  850. arXiv (Cornell University)

    Reinforcement-guided generative protein language models enable de novo design of highly diverse AAV capsids

    Lucas Ferraz, Ana F. Rodrigues, Pedro Giesteira Cotovio, Mafalda Ventura, Gabriela Silva, Ana Sofia Coroadinha, Miguel Machuqueiro, Cátia Pesquita

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 5.6 RL-based · 5.Function to Sequence

  851. bioRxiv (Cold Spring Harbor Laboratory)

    evedesign: accessible biosequence design with a unified framework

    Thomas A. Hopf, Artem Gazizov, Sergio Garcia Busto, Ethan Eschbach, SunJae Lee, Milot Mirdita, Rose Orenbuch, Khaoula Belahsen, David Ross, Chris Sander, Martin Steinegger, Simon d’Oelsnitz, Debora S. Marks

    Discovered via OpenAlex

  852. Analytical Chemistry

    Spatial Multiomics Combining Lipids and Gene Expression Using MALDI ISH MSI

    Kyle A. Vanderschoot, Jacob P. Padilla, Kelli A. Steineman, Christopher M. De Caro, Yongheng Wang, Aijun Wang, Marie C. Heffern, Elizabeth K. Neumann

    Discovered via OpenAlex

  853. De novo Design Protein Binders Targeting the Hydrophobic Surface of DENV4 and ZIKV NS1 Dimer

    Qi Pan, Geshu Zhang, Jianhai Yu, Wanqin Zhang, Shiqi Zhuang, Jingchuan Xue, Wei Zhao, Hongli Hu, Haizhan Jiao

    Discovered via OpenAlex

  854. ACS Catalysis

    Computer-Aided Directed Evolution Achieves Balanced Activity, Thermal Stability, and Selectivity in Stereoselective Carbonyl Reductase

    Jie Gu, Xin Su, Jun Wang, Yangqing Yu, Zhongzhen Li, Wanmeng Mu, Yan Xu, Yao Nie

    Discovered via OpenAlex

  855. PLANT PHYSIOLOGY

    AI-enabled protein design facilitates future plant research and crop breeding

    Yuxuan Lou, Tianhao Wu, Fan Xia, Anwen Zhao, Xiangfeng Wang

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 1. Reviews · 1.1 De novo protein design

  856. ACS Engineering Au

    Artificial Intelligence in Chemical Engineering: Protein Design from First Principles to Structural Prediction

    Joe Bailey, Soren C. Spina, Andrew Hu, Nathan Phan, Rachel B. Getman, Blaise R. Kimmel

    Discovered via OpenAlex

  857. Biologics

    De Novo Protein Design Enables Targeting of Intractable Oncogenic Protein–Protein Interfaces

    Varshika Ram Prakash, Yusuf Najy, Kalel Garrett, Brian F.P. Edwards, Benjamin L Kidder

    Discovered via OpenAlex

  858. ACM Computing Surveys

    Interpretable Machine Learning for Protein Science: Structure, Function, and Interactions

    Luiz Felipe Vecchietti, Minji Lee, Begench Hangeldiyev, Bryan Nathanael Wijaya, Hyunkyu Jung, Hahnbeom Park, Tae‐Kyun Kim, Meeyoung Cha, Ho Min Kim

    Discovered via OpenAlex

  859. Korean Society for Structural Biology

    YAPP-CD: yet another protein–peptide complex database

    Joon-Sang Park

    Discovered via OpenAlex

  860. Journal of Agricultural and Food Chemistry

    Artificial Intelligence-Driven Enzyme Engineering from Structural Prediction to De Novo Design

    Hongling Shi, Xueyang Bai, Fangyuan Tian, Yangwan Li, Dandan Li, Lunguang Yao, Chuang Xue, Cun‐Duo Tang

    Discovered via OpenAlex

  861. arXiv (Cornell University)

    Binary Latent Protein Fitness Landscapes for Quantum Annealing Optimization

    Truong-Son Hy

    Discovered via OpenAlex

  862. bioRxiv (Cold Spring Harbor Laboratory)

    Single-Pass Discrete Diffusion Predicts High-Affinity Peptide Binders at >1,000 Sequences per Second across 150 Receptor Targets

    Andre Watson

    Discovered via OpenAlex

  863. Current Opinion in Structural Biology

    De novo enzyme design: Controlling structure to design function

    Dina Listov, Sarel Jacob Fleishman

    Discovered via OpenAlex

  864. Journal of Chemical Information and Modeling

    Computational Mapping and Targeting of BK Channel Protein–Protein Interactions in Breast Cancer

    Mariela González‐Avendaño, Roberto Rosales‐Rojas, Ariela Vergara‐Jaque

    Discovered via OpenAlex

  865. Scientific Reports

    A generative explainable model for antimicrobial peptide prediction using bidirectional temporal convolutional neural network

    Farman Ali, Majdi Khalid, Raed A. I. Alsini, Ayman Yafoz, Tamim Alkhalifah, Mengze Du

    Discovered via OpenAlex

  866. bioRxiv (Cold Spring Harbor Laboratory)

    VarDCL: A Multimodal PLM-Enhanced Framework for Missense Variant Effect Prediction via Self-distilled Contrastive Learning

    Huiling Zhang, Ganzhang Zheng, Ziqi Xu, Haowen Zhao, Shaozhen Cai, Yuxiang Huang, Zihan Zhou, Yanjie Wei

    Discovered via OpenAlex

  867. Chem-Bio Informatics Journal

    ChEMBL-Derived Benchmark Dataset and Computational Results of Boltz-2-Based Binding Affinity Prediction

    Yugo Shimizu, Tatsuki Akabane, Masateru Ohta, Teruki Honma, Kazuyoshi Ikeda

    Discovered via OpenAlex

  868. Current Opinion in Structural Biology

    Artificial intelligence methods for protein structure and interaction prediction: Recent advances and challenges

    Alex Morehead, Jian Liu, Pawan Neupane, Jianlin Jack Cheng

    Discovered via OpenAlex

  869. arXiv (Cornell University)

    Protein Design with Agent Rosetta: A Case Study for Specialized Scientific Agents

    Jacopo Teneggi, SM Bargeen Alam Turzo, Tanya Marwah, Alberto Bietti, P. Douglas Renfrew, Vikram Khipple Mulligan, Siavash Golkar

    Discovered via OpenAlex

  870. arXiv (Cornell University)

    Refold: Refining Protein Inverse Folding with Efficient Structural Matching and Fusion

    Yiran Zhu, Changxi Chi, Hongxin Xiang, Wenjie Du, Xiaoqi Wang, Jun Xia

    Discovered via OpenAlex

  871. Probiotics and Antimicrobial Proteins

    Bridging Generative AI and Diffusion Models With Molecular Simulation to Design Anti-Quorum-Sensing De novo Peptides Targeting LasR of Pseudomonas aeruginosa

    Abbas Khan, Mona A. Sawali, Anwar Mohammad, Fakhrul Hasssan, Fahad M. Alshabrmi, Eid A. Alatawi, Sérgio Crovella, Dong‐Qing Wei, Abdelali Agouni

    Discovered via OpenAlex

  872. ACS Catalysis

    Enantiodivergent Evolution of a De Novo Protein for Enzymatic [2 + 2] Photocycloaddition Activity

    Benedikt B. Boesen, Anna Heider, Jack M. O’Shea, M. Groll, Thorsten Bach, Cathleen Zeymer

    Discovered via OpenAlex

  873. Journal of Biotechnology

    Deep learning revolutionizes protein research: Advances in structure prediction, functional annotation, and engineered design

    Jintong Zhang, Shengjie Wang, Le Gao, Qian Li

    Discovered via OpenAlex

  874. bioRxiv (Cold Spring Harbor Laboratory)

    ACENet: a graph neural network for predicting enzyme pHmin using structure and sequence insights

    Shantong Hu, Tong Pan, Jiayu Wang, Huan Yee Koh, Zhikang Wang, Yumeng Zhang, Lingxuan Zhu, Zhuoqian Li, Geoffrey I. Webb, Jiangning Song, Guimin Zhang

    Discovered via OpenAlex

  875. Nature Communications

    Impact of solvent forces and broken symmetry on the assembly of designed proteins at a liquid-solid interface

    Sakshi Yadav Schmid, Benjamin A. Helfrecht, Amy E. Stegmann, Benjamin A. Legg, Harley Pyles, Jiajun Chen, John R. Edison, Maxim A Ziatdinov, Zdeněk Preisler, Orion Dollar, Stephen Whitelam, Sergei V. Kalinin, David A. Baker, Christopher J. Mundy, Shuai Zhang, James J. De Yoreo

  876. Journal of Chemical Information and Modeling

    MAESD: A Unified Multi-Agent Evolutionary Framework for Protein Sequence Design

    Ze Song, Hailong Yang, Zhaohong Deng, Xiaoyong Pan, Hong Shen, Shudong Hu, Yanqi Zhong

    Discovered via OpenAlex

  877. arXiv (Cornell University)

    CHIMERA-Bench: A Benchmark Dataset for Epitope-Specific Antibody Design

    Mansoor Ahmed, Nadeem Taj, Imdadullah Khan, Hemanth Venkateswara, Murray Patterson

    Discovered via OpenAlex

  878. bioRxiv (Cold Spring Harbor Laboratory)

    Rational Design of Selective IL-2-based Activators for CAR T Cells Using AlphaFold3 and Physics-Informed Machine Learning

    Zakaria Larbi Dahmani, Anupam Banerjee

    Discovered via OpenAlex

  879. Protein Science

    AI ‐assisted design of a VEGFR2 agonistic peptide that promotes angiogenesis and wound repair

    Farzana Yasmeen, Rajath Ramachandran, Rameez Hassan Pirzada, B. I.W. CHOI, Hana Seo, Wook Kim, Moon Suk Kim, Sangdun Choi

    Discovered via OpenAlex

  880. arXiv (Cornell University)

    EvoFlows: Evolutionary Edit-Based Flow-Matching for Protein Engineering

    Nicolas Deutschmann, Constance Ferragu, Jonathan D. Ziegler, Shayan Aziznejad, Eli Bixby

    Discovered via OpenAlex

  881. Nano Letters

    Nanomolar Sensitivity Chirality Transfer from Designed Helical Repeat Proteins to Achiral CdS Nanorods

    Christopher D. Lowe, Le Tracy Yu, Jiaobing Tu, Isobelle O'Reilly, Emily Miura-Stempel, Helen C. Larson, Catherine Bodinger, David A. Baker, Brandi Michelle Cossairt

  882. PLoS Computational Biology

    Free energy perturbations in enzyme kinetic models reveal cryptic epistasis

    Karol Buda, Nobuhiko Tokuriki

    Discovered via OpenAlex

  883. eLife

    Amino acid homorepeats act as buffers to maintain proteostasis and constrain the compatible sequence space of proteomes

    Yukihiro Murase, Naoki Kitamura, Shotaro Namba, Ayano Satoh, Takashi T Makino, Ayako Moriya, Hisao Moriya

    Discovered via OpenAlex

  884. bioRxiv (Cold Spring Harbor Laboratory)

    A novel lipid-triggered allosteric site modulates LC3-LIR receptor binding activity

    Deepanshi Gahlot, Jesu Castin E, S C Mathur, Debajyoti Das, Ajit Kumar, Akanksha Arun, Chandrima Gain, Mridul Sharma, Ravi Kant Pal, Niyati Jain, Bichitra Kumar Biswal, Rajat Singh, Lipi Thukral

    Discovered via OpenAlex

  885. arXiv (Cornell University)

    Protein Counterfactuals via Diffusion-Guided Latent Optimization

    Weronika Kłos, Sidney Bender, Lukas Kades

    Discovered via OpenAlex

  886. The Journal of Biochemistry

    Observation of redistribution for local conformational dynamics in cross-reactive antibody design

    Yoshiki Yasuda, Satoru Nagatoishi, Jiei Sasaki, Ryo Matsunaga, Daisuke Kuroda, Takao Hashiguchi, Kouhei Tsumoto

    Discovered via OpenAlex

  887. Journal of Chromatography A

    Protein language model-guided generative design of affinity peptides for chromatographic purification of lentiviral vectors

    Feibo Wang, Xiaoyan Dong, Linling Yu, Yan Ping Sun, Qinghong Shi

    Discovered via OpenAlex

  888. bioRxiv (Cold Spring Harbor Laboratory)

    Automated extraction and optimization of protein purification protocols using multi-agent large language models

    Jeffery Ye, Amy E. DeRocher, Monique Khim, Sandhya Subramanian, Lisabeth Cron, Peter John Myler, Isabelle Phan

    Discovered via OpenAlex

  889. arXiv (Cornell University)

    How to make the most of your masked language model for protein engineering

    Calvin McCarter, Nick Bhattacharya, Sebastian W. Ober, Hunter Elliott

    Discovered via OpenAlex

  890. Nature Communications

    CF2H: a cell-free two-hybrid platform for rapid protein binder screening

    Julien Capin, Pauline Mayonove, Angelique DeVisch, A. Becher, Giang Ngo, Alexis Courbet, Robert J. Ragotte, Martin Cohen‐Gonsaud, Julien Espeut, J P Bonnet

    Discovered via OpenAlex

  891. Advances in Engineering Technology Research

    Review of AlphaFold3: A Groundbreaking Tool for Biomedical Applications

    Yihan Zhao

    Discovered via OpenAlex

  892. Nature Communications

    A paired sequence language model for protein-protein interaction modeling

    Jun Liu, Hungyu Chen, Yang Zhang

    Discovered via OpenAlex

  893. PLoS ONE

    Functional study of two flexible regions of the hepatitis E virus ORF1 replicase

    Léa Mézière, Sonia Fieulaine, Claire Montpellier, Martin Ferrié, Thibault Tubiana, Gabriel Vanegas Arias, Stéphane Bressanelli, Laurence Cocquerel, Cécile‐Marie Aliouat‐Denis

    Discovered via OpenAlex

  894. Advanced Science

    De Novo Multi‐Mechanism Antimicrobial Peptide Design via Multimodal Deep Learning

    Xiaojuan Li, Haifan Gong, Yue Wang, Yinuo Zhao, Lei Li, Peijing Bao, Qingzhou Kong, Jialu Fu, Boyao Wan, Yumeng Zhang, Jinghui Zhang, Jiekun Ni, Zhongxue Han, Xueping Nan, Kunping Ju, Longfei Sun, Yuerui Ma, Huijun Chang, Mengqi Zheng, Yanbo Yu, Xiaoyun Yang, Xiuli Zuo, Haina Wang, Yanqing Li

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 5.2 VAE-based · 5.Function to Sequence

  895. Biocatalysis and Biotransformation

    Applications and insights of NMR in enzyme engineering and biocatalysis

    Yolanda Pérez, Carlos J. Moreno, Pere Clapés

    Discovered via OpenAlex

  896. bioRxiv (Cold Spring Harbor Laboratory)

    What comes after de novo ? Automated lead optimization of proteins with CRADLE-1

    Eli Bixby, Gino Brunner, Daniel Danciu, Richard Dela Rosa, Nicolas Deutschmann, Constance Ferragu, Franziska Geiger, Christian Holberg, Patrick Kidger, Arthur Lindoulsi, Noé Lutz, Thomas McColgan, Sebastian Millius, Harmen van Rossum, Jinel Shah, Michelle Vandeloo, Paula Vidas, Harmen M. van Rossum, Jonathan D. Ziegler, Nicolò Baldi, Catalina IJspeert, Emanuele Monza, Angela I. Schriek

    Discovered via OpenAlex

  897. arXiv (Cornell University)

    Property-driven Protein Inverse Folding With Multi-Objective Preference Alignment

    Xiaoyang Hou, Junqi Liu, Chence Shi, Xin Liu, Zhi Yang, Jian Tang

    Discovered via OpenAlex

  898. Microorganisms

    Artificial Intelligence-Driven Discovery and Optimization of Antimicrobial Peptides Targeting ESKAPE Pathogens and Multidrug-Resistant Fungi

    Calina Wu-Mo, Ariana Flores-González, Jezrael Meléndez-Delgado, Valerie Ortiz-Gómez, Héctor Meléndez-González, Rafael Maldonado‐Hernández

    Discovered via OpenAlex

  899. Microbial Cell Factories

    Catalytically active inclusion bodies of Bacillus clausii laccase protein recombinantly produced in E. coli for dye decolorization

    Daniel Romero-Martínez, Francisco Gasteazoro, Luis Fernando Cofas‐Vargas, Enrique Garcia-Hernandez, Oscar González‐Davis, Guadalupe Zavala, Diego Rosiles-Becerril, Rafael Vázquez-Duhalt, Mauricio A. Trujillo‐Roldán, Norma A. Valdez‐Cruz

    Discovered via OpenAlex

  900. bioRxiv (Cold Spring Harbor Laboratory)

    Diffusion-ACP39: A Decoder-Adaptive Latent Diffusion Framework for Generative Anticancer Peptide Discovery

    Jielu Yan, Qichun Wu, YiFan Li, Jianxiu Cai, Mingliang Zhou, François‐Xavier Campbell‐Valois, Shirley W. I. Siu

    Discovered via OpenAlex

  901. arXiv (Cornell University)

    ProtAlign: Contrastive learning paradigm for Sequence and structure alignment

    Aditya Ranganath, Hasin Us Sami, Kowshik Thopalli, Bhavya Kailkhura, Wesam Sakla

    Discovered via OpenAlex

  902. bioRxiv (Cold Spring Harbor Laboratory)

    Miniprotein inhibitors of the Staphylococcus aureus efflux transporter NorA

    Priyanka Mishra, Adam M. Chazin-Gray, Gaëlle Lamon, David E. Kim, David A. Baker, Nathaniel J. Traaseth

    Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.3 RoseTTAFold-based

  903. Nature Communications

    Structural insights into insect-selective sodium channel toxins drive AI-enhanced biopesticide design

    Heng Jiang, Ruibo Gao, Huiqin Xu, Cheng Wang, Shuyue Ma, Yishu Gong, Lianyun Lin, Lina Yang, Xiang Li, Ye Liu, Rongcai Lu, Jun‐An Ma, Jinbo Xu, Ke Dong, Filip Van Petegem, Zheng Liu, Shaoying Wu, Zhiguang Yuchi

    Discovered via OpenAlex

  904. Journal of the American Chemical Society

    Hydrogen–Deuterium Exchange Mass Spectrometry Reveals an Antibody-Induced Allosteric Pathway Driving SARS-CoV-2 Spike Trimer Disassembly

    Yuxiang Luo, Banghui Liu, Ruijie Liu, Qiuluan Chen, Xiaoli Xiong, Huilin Li

    Discovered via OpenAlex

  905. bioRxiv (Cold Spring Harbor Laboratory)

    An Energy Landscape Approach to Miniaturizing Enzymes using Protein Language Model Embeddings

    Jakub Lála, Harsh Agrawal, Fanfei Dong, Jude Wells, Stefano Angioletti‐Uberti

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 2. Model-based design · 2.4 LLM-based

  906. bioRxiv (Cold Spring Harbor Laboratory)

    Co-designing sequence and structure of functional de novo enzymes with EnzyGen2

    Zhenqiao Song, Huichong Liu, Yunlong Zhao, Yang Yang, Lei Li

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.6 Transformer-based

  907. Biomacromolecules

    Unveiling the Intramolecular Thermodynamics of Multivalent Proteins: Exploratory Study on Engineered Protein Model

    Yu-na Kim, Bo-Hee Choi, Hyoin Park, Chan-Geun Kim, Yu‐Gon Eom, Yongwon Jung, Jeong‐Mo Choi

    Discovered via OpenAlex

  908. International Journal of Animal Biotechnology

    Foundation Artificial Intelligence Models in Animal Biotechnology: From Protein Structure Prediction to Genomic Language Models and Autonomous Laboratory Systems

    Anna Zhernakova, Santiago Marco‐Sola

    Discovered via OpenAlex

  909. Frontiers in Immunology

    Cloning, expression and characterisation of antigen-specific recombinant bat immunoglobulin from the black flying fox (Pteropus alecto)

    Jun Jet Hen, Ariel Isaacs, Benjamin Liang, Tony Schountz, Keith Joseph Chappell, Paul R. Young, Naphak Modhiran, Daniel Watterson

    Discovered via OpenAlex

  910. Zenodo (CERN European Organization for Nuclear Research)

    Full-Atom Peptide Design via Riemannian–Euclidean Bayesian Flow Networks

    Hao Qian

    Discovered via OpenAlex

  911. arXiv (Cornell University)

    AbAffinity: A Large Language Model for Predicting Antibody Binding Affinity against SARS-CoV-2

    Faisal Bin Ashraf, Animesh Ray, Stefano Lonardi

    Discovered via OpenAlex

  912. Nature

    Genetically encoded assembly recorder temporally resolves cellular history

    Yuqing Yan, Jiaxi Lu, Zhe Li, Zuohan Zhao, Timothy F. Shay, Shunzhi Wang, Yaping Lei, Yimei Wang, Wei Chen (23863), Patrick Parker, Hongru Yang, Aileen Qi, Yongzhi Sun, Dwight E. Bergles, David A. Baker, Dingchang Lin

  913. arXiv (Cornell University)

    Deep learning-guided evolutionary optimization for protein design

    Erik Hartman, Di Tang, Johan A. Malmström

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 7. Other tasks · 7.1 Effects of mutation & Fitness Landscape

  914. Biosensors and Bioelectronics

    Designed peptides as affinity ligands for extracellular-vesicle-based cancer diagnosis

    Sudeep Sarma, Jinho Park, Young Kwan Cho, Arpan Tapdiya, Hyun-Kyung Woo, Hakho Lee, Carol K. Hall

    Discovered via OpenAlex

  915. bioRxiv (Cold Spring Harbor Laboratory)

    Structural Plausibility Without Binding Specificity: Limits of AI-Based Antibody-Antigen Structure Prediction Confidence Scores

    Eva Smorodina, Montader Ali, Klara Kropivšek, Leonardo Salicari, Samo Miklavc, Aibek Kappassov, Chengcheng Fu, Pietro Sormanni, Ario de Marco, Victor Greiff

    Discovered via OpenAlex

  916. arXiv (Cornell University)

    Rigidity-Aware Geometric Pretraining for Protein Design and Conformational Ensembles

    Zhanghan Ni, Yanjing Li, Zeju Qiu, Bernhard Schölkopf, Hongyu Guo, Weiyang Liu, Shengchao Liu

    Discovered via OpenAlex

    Preprint source: bioRxiv: Bioinformatics

    Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.8 Flow-based

  917. bioRxiv (Cold Spring Harbor Laboratory)

    High Diversity Gene Libraries Facilitate Machine Learning Guided Exploration of Fluorescent Protein Sequence Space

    Anissa Benabbas, Phillip Kearns, Avery Billo, Lauren O. Chisholm, Calin Plesa

    Discovered via OpenAlex

  918. International Research Journal of Modernization in Engineering Technology and Science

    An Intelligent Genetic Algorithm–Based System for Automated University Course Allocation

    Discovered via OpenAlex

  919. bioRxiv (Cold Spring Harbor Laboratory)

    EnzySeek: Efficient Exploration of Enzyme Reaction Pathways Using AI Agents

    Kang Xu, Tao Yu, Kangwei Xu, Chenxu Liu, Rongjie Wu

    Discovered via OpenAlex

  920. RUNG

    Structural plausibility without binding specificity

    Eva Smorodina, Montader Ali, Klara Kropivšek, Leonardo Salicari, Samo Miklavc, Chengcheng Fu, Pietro Sormanni, Ario De Marco, Victor Greiff

    Discovered via OpenAlex

  921. arXiv (Cornell University)

    On the Reliability of AI Methods in Drug Discovery: Evaluation of Boltz-2 for Structure and Binding Affinity Prediction

    Shunzhou Wan, Xibei Zhang, Xue Xiao, Peter V. Coveney

    Discovered via OpenAlex

  922. Computational and Structural Biotechnology Journal

    Adversarial Sequence Mutations in AlphaFold and ESMFold Reveal Nonphysical Structural Invariance, Confidence Failures, and Concerns for Protein Design

    Jonathan Feldman, Maximilian Brogi, Jeffrey Skolnick

    Discovered via OpenAlex

  923. Computational and Structural Biotechnology Journal

    BioPipelines: Accessible Computational Protein and Ligand Design for Chemical Biologists

    Gianluca Quargnali, Pablo Rivera‐Fuentes

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.3 RoseTTAFold-based

  924. Zenodo (CERN European Organization for Nuclear Research)

    The AI Revolution in Protein Science Current Status and Future Prospects for Biopharmaceutical Applications

    Yutong Nan

    Discovered via OpenAlex

  925. Journal of physiological investigation.

    Generative Protein Design for Physiological Intervention: Progress and Horizons

    Po‐Jung Chien, Chyuan-Chuan Wu

    Discovered via OpenAlex

  926. Computational and Structural Biotechnology Journal

    Protein Design Enters the Artificial Intelligence Era: Foundations, Tools, and Emerging Paradigms

    Yanlin Mi, Arpit Shukla, Mark Tangney, Sabin Tabirca, Venkata V. B. Yallapragada

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 1. Reviews · 1.1 De novo protein design

  927. Briefings in Bioinformatics

    Generative design and validation of therapeutic peptides for glioblastoma based on a potential target ATP5A

    Hao Qian, Pu You, Lin Zeng, Jingyuan Zhou, Dengdeng Huang, Kaicheng Li, Shikui Tu, Lei Xu

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.8 Flow-based

  928. Molecular Plant Pathology

    Protein Language Model‐Driven Optimisation of Antimicrobial Peptide Pth‐Ca1 Against Pectobacterium brasiliense Using ESMFold ‐Predicted Structures and the ESM ‐3 Model

    Linhui Song, Ge Zhang, Mengying Hua, Jingna Yuan, Jian Wu, Hao Wang, Fei Yan, Jiejun Peng

    Discovered via OpenAlex

  929. Briefings in Bioinformatics

    SaMCL: a multi-task collaborative learning framework for peptide-protein interaction prediction based on structure-aware protein language models

    Siyi He, Dongzhen Tang, Tiantian Zhu, Zexuan Zhu, Yumeng Liu, J Zhang

    Discovered via OpenAlex

  930. bioRxiv (Cold Spring Harbor Laboratory)

    Structure-guided generative design of peptides targeting the FtsQBL divisome complex inhibit Escherichia coli cell division

    Pauline Remont, Xiaosong Liu, Federico Croci, Ariel Méchaly, Gouzel Karimova, Minh-Ha Nguyen, Iñaki Guijarrro, Marilyne Davi, Cécile Guillon, Constantin Bogdan Ciambur, Fabrice Agou, Alix Boucharlat, Ahmed Haouz, Jeanne Chiaravalli, Daniel Ladant, Olivier Spérandio

    Discovered via OpenAlex

  931. Preprints.org

    A Comprehensive Survey of Multimodal LLMs for Scientific Discovery

    Liang Yan, Xu Jiang, Jian Ma, Yuhang Liu, Tian Bian, Qichao Wang, Abhishek Basu, Yu Rong, Tingyang Xu, Pengcheng Wu, Le Song, Imran Razzak, Junchi Yan, Zengfeng Huang, Yutong Xie

    Discovered via OpenAlex

  932. FEBS Journal

    Elucidating the catalytic mechanism of a previously undescribed carbohydrate esterase family 7 acetyl xylan esterase ( LaCE7A )

    Ang Lv, Junwen Ma, Ling Wang, Chu Wang, Qiaojuan Yan, Weiwei Han, Zhengqiang Jiang, Shaoqing Yang

    Discovered via OpenAlex

  933. Frontiers in Pharmacology

    Antibody-enabled structural biology and AI-driven antibody design

    Khuram U. Ashraf, Satchal K. Erramilli

    Discovered via OpenAlex

  934. Small

    Engineered Protein‐Cellulose Composite Hydrogels with Superior Mechanical Performance for Bioadhesion

    Juya Jeon, Zhenqin Wang, Huiyong Li, Manjula Senanayake, Sai Venkatesh Pingali, Hanxun Jin, Kok Zhi Lee, Shri Venkatesh Subramani, Larisa Belaygorod, Batool Arif, Ying Yu, Guy M. Genin, Marcus B. Foston, Mohamed Adel Zayed, Fuzhong Zhang

    Discovered via OpenAlex

  935. Current Opinion in Structural Biology

    De novo engineering of protein interactions: Retrospective and current advances

    Alisa Khramushin, Evgenia Elizarova, Bruno E. Correia

    Discovered via OpenAlex

  936. Biotechnology Advances

    Computational dual-loop frameworks bridging single-enzyme design and cascade tunnel network engineering for next-generation biosynthetic systems

    Yangyang Li, Guocheng Du, Jianzhong Chen, Xueqin Lv, Long Liu

    Discovered via OpenAlex

  937. bioRxiv (Cold Spring Harbor Laboratory)

    FAF1 and FAF2 enhance human p97-UFD1-NPL4 complex unfoldase activity enabling rational design of p97 activators

    Pritha Dasgupta, Ian R. Kelsall, Gaurav Anand, Anna Pérez‐Ràfols, Axel Knebel, Robert Gourlay, Glenn Robert Masson, Yogesh Kulathu

    Discovered via OpenAlex

  938. bioRxiv (Cold Spring Harbor Laboratory)

    Rapid sequence-based screening of structure-disrupting protein mutations

    Jaemin Oh, Xiaoning Qian, Byung-Jun Yoon

    Discovered via OpenAlex

  939. ACS Catalysis

    Fluorescent Biosensor-Guided Engineering of Enzyme Cascades for Electrochemical Applications

    Nathan J. Ricks, Monica Brachi, FNU Arun, Egor Baiarashov, Shelley D. Minteer, Ming Chen Hammond

    Discovered via OpenAlex

  940. Microbial Cell Factories

    Combining computer-aided enzyme design and chromosomal integration for plasmid-free biosynthesis of 1,5-pentanediol in Escherichia coli

    Hongyu Deng, Jing Wang, Fei Meng, Chunling Ma, Piwu Li, Junqing Wang, Xiaonan Wang, Chunhui Zhao, Yan Zhang, Ruiming Wang, Ning Chen

    Discovered via OpenAlex

  941. Research Square

    In Silico Design of a Multimodal Trimeric Peptide Candidate Predicted to Simultaneously Target Glycemic Control, Autoimmunity, and Pancreatic β-Cell Regeneration in Type 1 Diabetes

    Luís Jesuíno de Oliveira Andrade, Gabriela C. Matos de Oliveira, Luís Matos de Oliveira

    Discovered via OpenAlex

  942. Nature Machine Intelligence

    Conditional diffusion with locality-aware modal alignment for generating diverse protein conformational ensembles

    Baoli wang, Chenglin Wang, Jingyang Chen, Danlin Liu, Changzhi Sun, Jie Zhang, Kai Zhang, Honglin Li

    Discovered via OpenAlex

  943. bioRxiv (Cold Spring Harbor Laboratory)

    FLIP2: Expanding Protein Fitness Landscape Benchmarks for Real-World Machine Learning Applications

    Kieran Didi, Sarah Alamdari, Alex Xijie Lu, Bruce J. Wittmann, Kadina E. Johnston, Ava P. Amini, Ali Madani, Maya Czeneszew, Christian Dallago, Kevin K. Yang

  944. eLife

    Defining the chromatin-associated protein landscapes on Trypanosoma brucei repetitive elements using synthetic TALE proteins

    Roberta Carloni, Tadhg Devlin, Pin Tong, Christos Spanos, Tanya Auchynnikava, Juri Rappsilber, Keith R. Matthews, Robin C. Allshire

    Discovered via OpenAlex

  945. bioRxiv (Cold Spring Harbor Laboratory)

    A Comprehensive Atlas and Machine-Learning Framework for Predicting IDR-Protein Binding Affinity

    Subinoy Adhikari, Soham Choudhuri, Jagannath Mondal

    Discovered via OpenAlex

  946. SLAS DISCOVERY

    Binder2030: a quantitative membrane proteome binding dataset enabling AI-driven drug discovery

    Naoki Tarui, Masaharu Nakayama, Thuy Duong Nguyen

    Discovered via OpenAlex

  947. Protein Science

    Deamidation and isomerization to elusive isoaspartate in a computationally designed miniprotein

    Katerina M. Blejec, Colin A. Smith

    Discovered via OpenAlex

  948. Pharmaceutics

    Discovery of Peptide-Based Tubulin Inhibitors Through Structure-Guided Design

    Nicolás Osses-Bagatello, Esteban Rocha-Valderrama, José Ortega-Campos, Mauricio Moncada‐Basualto, Matías Zúñiga-Bustos

    Discovered via OpenAlex

  949. bioRxiv (Cold Spring Harbor Laboratory)

    Rational design of synthetic proteins using a genome-scale CRISPR screen

    Wells H. Burrell, Simon J. Mueller, Zharko Daniloski, P. Duffy Doyle, Anne Bruun Rovsing, Christopher James, Max Drabkin, Chien-Yu Chou, Hei Yu Annika So, Lyla Katgara, Akash Sookdeo, Lu Lu, Georges-Ibrahim Cisse, Rachel E Yan, Neville E. Sanjana

    Discovered via OpenAlex

  950. PLoS Computational Biology

    Controllable protein design via autoregressive direct coupling analysis conditioned on principal components

    Francesco Caredda, Lisa Gennai, Paolo De Los Rios, Andrea Pagnani

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 5.10 Autoregressive-models · 5.Function to Sequence

  951. Cell

    Unified modeling of 3D molecular generation via atomic interactions with PocketXMol

    Xingang Peng, Ruihan Guo, Fenglin Guo, Ziyi Wang, Jiayu Sun, Jiaqi Guan, Yinjun Jia, Yan Xu, Yanwen Huang, Muhan Zhang, Jian Peng, Xinquan Wang, 韩传慧, Zihua Wang, Jianzhu Ma

    Discovered via OpenAlex

  952. bioRxiv (Cold Spring Harbor Laboratory)

    ProtFlow: Flow Matching-based Protein Sequence Design with Comprehensive Protein Semantic Distribution Learning and High-quality Generation

    Zitai Kong, Yiheng Zhu, Yinlong Xu, Mingze Yin, Tingjun Hou, Jian Wu, Hongxia Xu, Chang‐Yu Hsieh

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 5.7 Flow-based · 5.Function to Sequence

  953. Proceedings of the National Academy of Sciences

    Pichia-CLM: A language model–based codon optimization pipeline for Komagataella phaffii

    Harini Narayanan, John Christopher Love

    Discovered via OpenAlex

  954. bioRxiv (Cold Spring Harbor Laboratory)

    Large-scale exploration of protein space by automated NMR

    Thomas Müntener, Dylan Abramson, Elsa Stern, Ines Hertel, Gytis Jankevicius, Guillaume Mas, Gert E. Folkers, Basile I. M. Wicky, Sebastian Hiller

    Discovered via OpenAlex

  955. Proteins Structure Function and Bioinformatics

    AlphaFold2 ‐Guided Cyclic Peptide Stabilizer Design to Target Protein–Protein Interactions

    Niklas Halbwedl, Martin Zacharias

    Discovered via OpenAlex

  956. arXiv (Cornell University)

    MAC-AMP: A Closed-Loop Multi-Agent Collaboration System for Multi-Objective Antimicrobial Peptide Design

    Gen Zhou, Sugitha Janarthanan, Lianghong Chen, Pingzhao Hu

    Discovered via OpenAlex

  957. Research Square

    Enhancing the Comprehensive Stability of Candida parapsilosis Carbonyl Reductase in Biphasic Systems through Rational Protein Design

    Gang Cao, Yucai Lü, Ting Song, Xianwu Qin, Zhiying Tu, Jinling Guo, Huajun Luo, Dachun Gong

    Discovered via OpenAlex

  958. bioRxiv (Cold Spring Harbor Laboratory)

    Enhancing ML-based binder design with high-throughput screening: a comparison of mRNA and yeast display technologies

    Zhiyuan Yao, McGuire Metts, Avery K. Huber, J Li, Tomoaki Kinjo, Henry Dieckhaus, Amrita Nallathambi, Albert A. Bowers, Brian A. Kuhlman

    Discovered via OpenAlex

  959. International Journal of Pure Science Research Studies (IJPSRS)

    Crispr-Based catalysts for selective bond activation

    Kesavan K

    Discovered via OpenAlex

  960. Zenodo (CERN European Organization for Nuclear Research)

    Active Molecular Interception: De Novo Designed Proteins as a New Paradigm in the Management of Uremic Toxins

    Orlando Samayoa Montiel

    Discovered via OpenAlex

  961. arXiv (Cornell University)

    Cross-Chirality Generalization by Axial Vectors for Hetero-Chiral Protein-Peptide Interaction Design

    Ziyi Yang, Zitong Tian, Yinjun Jia, Tianyi Zhang, Jiqing Zheng, Hao Wang, Yubu Su, Juncai He, Lei Liu, Yanyan Lan

    Discovered via OpenAlex

  962. Computers in Biology and Medicine

    Overcoming structural complexity in Galectin-3BP through an integrative computational antibody design workflow

    Andrielly Henriques Santos-Costa, Eduardo Menezes Gaieta, Aline O. Albuquerque, Julia Silva Souza, Diego S. Almeida, Jean Vieira Sampaio, Patrick England, G. Sartori, João Hermínio Martins da Silva

    Discovered via OpenAlex

  963. mAbs

    Balancing the extremes for antibody developability: hydrophobic and electrostatic germline framework signatures for CDR-loop compensation

    Vera A. Spanke, Valentin J. Hoerschinger, Clarissa A. Seidler, Katharina B. Kroell, Vincent Wieser, Sabine Imhof-Jung, Benjamin Weiche, Alexander Bujotzek, Guy J. Georges, Klaus Roman Liedl

    Discovered via OpenAlex

  964. Current Opinion in Structural Biology

    Rational protein design

    Joel J. Chubb, Aimee L. Boyle, Katherine I. Albanese

    Discovered via OpenAlex

  965. Protein Science

    MemPPI platform for measuring and engineering membrane protein–protein interactions in mammalian cells via split nanoluciferase

    Weiyi Tang, Sebastian Jojoa-Cruz, Jiayi Li, George Goldenfeld, Marco Mravic

    Discovered via OpenAlex

  966. SynBio

    Albumin-Binding Domains in Therapeutic Protein Engineering: A Structural and Computational Perspective on Rational Design

    Matthew Argyle, Dallin Chipman, Anna Claire Woolley, Bradley Charles Bundy, Dennis Della Corte

    Discovered via OpenAlex

  967. Marine Drugs

    From Host-Derived Pressures to the Environmental Anti-Antimicrobial Peptides Resistome: Mechanisms, Reservoirs and Implications for Therapeutic Peptide Design

    Yi Lu, Baomei Zhang, Zishuo Wang, Yidi He, Hezi Ge, Hongyue Ma, Pengfei Cui

    Discovered via OpenAlex

  968. Polymers

    Smart Antibiofilm Platforms Based on Synthetic Antimicrobial Peptides-Engineered Hydrogels

    Rahela Carpa, Bogyor Agota-Katalin, Anca Livia Butiuc-Keul

    Discovered via OpenAlex

  969. ChemRxiv

    Embedding-Guided Design Rules for Programmable Mitochondrial Protein Import and Modular Organelle Organization

    Mark I.R. Petalcorin

    Discovered via OpenAlex

  970. Briefings in Bioinformatics

    De novo functional protein sequence generation: overcoming data scarcity through regeneration and large language models

    Chenyu Ren, Daihai He, Jian Huang

    Discovered via OpenAlex

  971. bioRxiv (Cold Spring Harbor Laboratory)

    Reading TEA leaves for de novo protein design

    Lorenzo Pantolini, Janani Durairaj

    Discovered via OpenAlex

  972. bioRxiv (Cold Spring Harbor Laboratory)

    A Systematic Benchmark for Peptide Property Prediction

    Xiaoying Dong, Yang Kaijun, Wu Tianxiang, Pengyong Li, Lin Gao

    Discovered via OpenAlex

  973. bioRxiv (Cold Spring Harbor Laboratory)

    Generalise or Memorise? Benchmarking Ligand-Conditioned Protein Generation from Sequence-Only Data

    Alex Vicente, L Dornfeld, Joan Coines, Noelia Ferruz

    Discovered via OpenAlex

  974. International Journal of Molecular Sciences

    Improving the Thermostability of the Qβ Bacteriophage Coat Protein Through Single-Site Mutation Based on Molecular Dynamics

    Meng Qu, Mingyu Li, Jing Sun, Yanhua Jiang, Wenjia Zhu, Yingying Guo, Li Na, Dapeng Wang, Lin Yao

    Discovered via OpenAlex

  975. bioRxiv (Cold Spring Harbor Laboratory)

    Decoupling Structure and Property in Discrete Protein Diffusion: Alignment Dynamics and Collapse Mechanisms

    Junqi Wu, Liyan Dong, Nuo Jia, Longyu Li, Hao Zhang

    Discovered via OpenAlex

  976. arXiv (Cornell University)

    TerraBind: Fast and Accurate Binding Affinity Prediction through Coarse Structural Representations

    Matteo Rossi, Ryan D. Pederson, Miles Wang-Henderson, Ben Kaufman, Edward Williams, Carl Underkoffler, Owen Lewis Howell, Adrian Layer, Stephan Thaler, Narbe Mardirossian, John Parkhill

    Discovered via OpenAlex

  977. Journal of Chemical Information and Modeling

    Subtimizer: Computational Workflow for Structure-Guided Design of Potent and Selective Kinase Peptide Substrates

    Abeeb Abiodun Yekeen, Cynthia J. Meyer, Melissa K. McCoy, Bruce A. Posner, Kenneth D. Westover

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 4.5 GNN-based · 4.Scaffold to Sequence

  978. Crop Design

    Translational potential of AI-driven de novo protein binders for crop protection and improvement

    Mahmudul Hasan Rifat, Li Tai, Yukang Wang, Qianwen Deng, Ronghui Pan, Yanlei Feng

    Discovered via OpenAlex

  979. arXiv (Cornell University)

    SaDiT: Efficient Protein Backbone Design via Latent Structural Tokenization and Diffusion Transformers

    Shentong Mo, Lanqing Li

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 3. Function to Scaffold · 3.4 Diffusion-based

  980. Zenodo (CERN European Organization for Nuclear Research)

    A roadmap for AI-driven protein design

    Miguel Ángel González Arias

    Discovered via OpenAlex

  981. Journal of the American Chemical Society

    Mesostructured Water Enhances Stability of ProteinMPNN-Designed Ubiquitin-Fold Proteins

    Lu-Yi Chen, Wei-Lin Lu, Tanvi Pathania, I-Hsuan Chu, Meng‐Ru Ho, Wei-Chen Chuang, Yuan‐Chao Lou, Ta I Hung, Yohei Miyanoiri, Chia‐en A. Chang, Kuen‐Phon Wu

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 4.5 GNN-based · 4.Scaffold to Sequence

  982. Journal of Translational Medicine

    De novo protein design: a transformative frontier in clinical protein applications

    Jie Gao, Zaiyong Zheng, Xueting Yu, Yamei Luo, Yang Yu, Chunxiang Zhang

    Discovered via OpenAlex

  983. bioRxiv (Cold Spring Harbor Laboratory)

    Designing protein/non-protein binding interactions using a full-atom diffusion model

    Kale Kundert, George McDonald Church

    Discovered via OpenAlex

  984. arXiv (Cornell University)

    RIGA-Fold: A General Framework for Protein Inverse Folding via Recurrent Interaction and Geometric Awareness

    Sisi Yuan, Jiehuang Chen, Junchuang Cai, Dong Xu, Xueliang Li, Zexuan Zhu, Junkai Ji

    Discovered via OpenAlex

  985. bioRxiv (Cold Spring Harbor Laboratory)

    Computational design of blue melanin with peptide motif scaffolding

    Di Sheng Lee, Bomi Park, Sergio Salgado, James Dolgin, David Lee Kaplan

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.3 RoseTTAFold-based

  986. arXiv (Cornell University)

    Generative AI for Enzyme Design and Biocatalysis

    Lasse Middendorf, Noelia Ferruz

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 1. Reviews · 1.5 Enzyme design

  987. JACS Au

    Harnessing AI for Antimicrobial Peptide Innovation against Multidrug Resistance

    João P. F. Pimentel, Raquel M. Q. Orozco, Samilla Beatriz de Rezende, Lucas Lima, Marlon Henrique e Silva Cardoso

    Discovered via OpenAlex

  988. Molecules

    Antimicrobial Peptide Nanoassemblies: Design, Response Mechanisms, and Biomedical Applications

    Wang Tao, Linbao Ji, Yucheng Zhang, Zhili Niu, Xiaoyi Jiang, Xingyao Wang, Qingtai Zhang, Yuting Zhang, Peng Tan, Yue Feng, Xi Ma, Zhihong Sun

    Discovered via OpenAlex

  989. Critical Reviews in Biotechnology

    Design of novel enzymes with the incorporation of noncanonical amino acids

    Liang Cheng, Lirong Yang, Zhongdi Song, Haoran Yu

    Discovered via OpenAlex

  990. arXiv (Cornell University)

    A Systematic Evaluation of Co-folding Model Representations for Small-Molecule Learning

    Hyosoon Jang, Hyunjin Seo, Honghui Kim, Seonghyun Park, Taewon Kim, Yunhui Jang, Sungsoo Ahn

    Discovered via OpenAlex

  991. The Crop Journal

    Biological nitrogen and carbon fixation: Bridging the gap between synthetic symbioses and synthetic biology

    Qi Cheng, C.C. Ma, Xuelu Wang

    Discovered via OpenAlex

  992. Genomics Proteomics & Bioinformatics

    Benchmarking Generative AI Protein Models Reveals Differences Between Structural and Sequence-based Approaches

    Alexander J Barnett, Rajendra KC, Pratikshya Pandey, Pamodha Somasiri, Kirsten A. Fairfax, Sandy S. C. Hung, Alex William Hewitt

    Discovered via OpenAlex

  993. Biochemical Society Transactions

    Designing de novo TIM barrels: insights into stabilization, diversification, and functionalization strategies

    Julian Beck, Sergio Romero‐Romero

    Discovered via OpenAlex

  994. Neuroscience

    The mitochondria-targeted peptide HDAP2 reduces mitochondrial loss and retinal ganglion cell degeneration after optic nerve injury

    Margaret A. MacNeil, Sara Arain, Widnie Mentor, Virginia García‐Marín, Alexander Victor Birk

    Discovered via OpenAlex

  995. Natural Product Communications

    Antimicrobial Peptides and Artificial Intelligence: Promising Tools for Sustainable Agriculture Practices

    Lina Blandón, Andrea Mesa, Sergio Andrés Orduz

    Discovered via OpenAlex

  996. International Journal of Pharmaceutical and Clinical Research

    Greener and cleaner: The industrial potential of cold-active and Alkaliphilic proteases

    Ankana Ghosh, Pritha Pal

    Discovered via OpenAlex

  997. bioRxiv (Cold Spring Harbor Laboratory)

    An AI-Native Biofoundry for Autonomous Enzyme Engineering: Integrating Active Learning with Automated Experimentation

    Chuwen Zhang, Lixiang Yang, Yanjia Qin, Danjing Li, Shimao Dong, Meng Yang

    Discovered via OpenAlex

  998. Communications Biology

    Characterising nanobody developability to improve therapeutic design using the Therapeutic Nanobody Profiler

    G. Gordon, João Henrique Diniz Brandão Gervásio, Colby Souders, Charlotte Mary Deane

  999. bioRxiv (Cold Spring Harbor Laboratory)

    Topological reprogramming transforms an integral membrane oligosaccharyltransferase into a water-soluble glycosylation catalyst

    Yong Hyun Kwon, Ljubica Mihaljević, Keehun Kim, David E. Kim, Thomas Connor Donahue, Erik J. Bidstrup, Chandra Kanth Bandi, Belen Sotomayor, Sophia W. Hulbert, Kathryn A. A. Myers, Anru Tian, Mariah Culpepper, Dario Mizrachi, Thapakorn Jaroentomeechai, Henrik Clausen, Michael C. Jewett, David A. Baker, Matthew P. DeLisa

  1000. Acta Pharmaceutica Sinica B

    Artificial intelligence in biologic drug discovery: A review of methodological evolution and therapeutic applications

    Jianxin Tang, Daohong Gong, Honglin Li, Shiliang Li

    Discovered via OpenAlex

  1001. bioRxiv (Cold Spring Harbor Laboratory)

    Nab-paclitaxel fused with the de novo designed receptor binder exhibits enhanced tumor targeting and therapeutic efficacy

    Yuanying Qian, Weikang Yan, Fan Xu, Yali Liu, Fabao Chen, Yue Lu, Zihan Zhang, Ao Gu, Ruobing Yu, Zhen Fang, Yang Yu, Maolan Li, Longxing Cao, Yingbin Liu, Yongning He

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 4.5 GNN-based · 4.Scaffold to Sequence

  1002. Bioactive Materials

    Artificial intelligence driven protein design and sustainable nanomedicine for advanced theranostics

    Donya Esmaeilpour, Michael Richard Hamblin, Jianlin Cheng, Arezoo Khosravi, Jian Liu, Atefeh Zarepour, Ali Zarrabi, Mika Sillanpaa, Ehsan Nazarzadeh Zare‬, Jianliang Shen, Hassan Karimi-Maleh

    Discovered via OpenAlex

  1003. Bioinformatics

    Multi-scale structural similarity embedding search across entire proteomes

    Joan Segura, Rubén Sánchez-García, Sebastian Bittrich, Yana Rose, Stephen Kevin Burley, José M. Duarte

    Discovered via OpenAlex

  1004. Frontiers in Artificial Intelligence

    KmPred: prediction of Michaelis constants (Km) using an integrative machine learning framework

    Meshari Alazmi

    Discovered via OpenAlex

  1005. arXiv (Cornell University)

    Minimal-Action Discrete Schrödinger Bridge Matching for Peptide Sequence Design

    Shrey Goel, Pranam Chatterjee

  1006. bioRxiv (Cold Spring Harbor Laboratory)

    The missing link between biomolecular condensates and amyloid fibrils

    Art Hoti, Shuya Zang, Ephraim Prantl, Michele Grünewald, Alexander Kros, Herre Jelger Risselada, G. J. A. Sevink

    Discovered via OpenAlex

  1007. Zenodo (CERN European Organization for Nuclear Research)

    Deep learning enables accurate design of functional transmembrane proteins

    Bo Zhang, Chunfu Xu

    Discovered via OpenAlex

  1008. bioRxiv (Cold Spring Harbor Laboratory)

    An Artificial Intelligence-based framework for protein interaction design with accelerated KAN-based Positive-Unlabeled learning

    Shubhrangshu Ghosh, Pralay Mitra

    Discovered via OpenAlex

  1009. arXiv (Cornell University)

    ProDCARL: Reinforcement Learning-Aligned Diffusion Models for De Novo Antimicrobial Peptide Design

    Fang Sheng, Mohammad Noaeen, Zahra Shakeri

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 4.12 RL-based · 4.Scaffold to Sequence

  1010. ChemRxiv

    A new benchmark for deep learning based affinity prediction: Solving the inter-protein scoring noise problem

    Malte Grieswelle, Samuel K. R. Homberg, Philipp Janssen, Jürgen Kaminski, Joana Massa, Ann‐Kathrin Prinz, S. Georgiev, Oliver Koch

    Discovered via OpenAlex

  1011. Proceedings of the National Academy of Sciences

    Mapping targetable sites on the human surfaceome for the design of novel binders

    Petra E. M. Balbi, Ahmed Sadek, Anthony Marchand, Ta-Yi Yu, Jovan Damjanovic, Sandrine Georgeon, Joseph H. Schmidt, Simone Fulle, Che Yang, Hamed Khakzad, Bruno E. Correia

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.4 CNN-based

  1012. Journal of the American Chemical Society

    Enzyme-Responsive Hemostatic Elastin-like Polypeptides for Fibrin Stabilization and Coagulation Restoration in Thrombocytopenia

    Yang Sun, Shin-Hae Kang, Malvina Heiniger, Ivan Urosev, Rosario Vanella, Adrian Bertschi, Michael A. Nash

    Discovered via OpenAlex

  1013. Infoscience (Ecole Polytechnique Fédérale de Lausanne)

    Mapping targetable sites on the human surfaceome for the design of novel binders

    Petra E. M. Balbi, Ahmed K. Sadek, Anthony Marchand, Ta-Yi Yu, Jovan Damjanovic, Sandrine Georgeon, Joseph Schmidt, Simone Fulle, Che Yang, Hamed Khakzad, Dominik Niopek

    Discovered via OpenAlex

  1014. ChemRxiv

    CO₂ Responsive Nanoscopic and Macroscopic Materials Directed by Peptides

    Tannaz Farrokhi, Stephanie Ceballos, Samantha Silva, Michael B. Ross

    Discovered via OpenAlex

  1015. Bioconjugate Chemistry

    Screening and Engineering of Ancestral Sortase Es That Enable High-Fidelity Enzyme Design with Activity Trade-Off

    Ryoma Koshiba, Taichi Chisuga, Daisuke Fujinami, Hiroyuki Takeda, Shogo Nakano

    Discovered via OpenAlex

  1016. Nature Chemical Biology

    De novo design of potent CRISPR–Cas13 inhibitors

    Cyntia Taveneau, Her Xiang Chai, Jovita D’Silva, Rebecca S. Bamert, Honglin Chen, Brooke K. Hayes, Roland W. Calvert, Jacob Purcell, Daniel J. Curwen, Fabian Munder, Lisandra L. Martin, Jeremy J. Barr, Joseph Rosenbluh, Mohamed Fareh, Rhys Grinter, Gavin J. Knott

    Discovered via OpenAlex

  1017. bioRxiv (Cold Spring Harbor Laboratory)

    Overcoming systematic data biases enables accurate prediction of enzyme k cat fold-changes for computational protein design

    Yvan Rousset, Alexander Kroll, Martin J. Lercher

    Discovered via OpenAlex

  1018. bioRxiv (Cold Spring Harbor Laboratory)

    Surf2Spot: A Surface-Informed Geometry-Aware Model for Predicting Binder and Nanobody Design Hotspots

    Anwen Zhao, Yu Li, Tianhao Wu, Ran Fu, Zixuan Wang, Yanfen Xu, Xuliang Han, Yuxuan Lou, Wenying Wang, Jun Yan, Xiangfeng Wang

    Discovered via OpenAlex

  1019. Advanced Science

    Protein Language Model‐Guided Engineering of a 2,3‐Butanediol Dehydrogenase for the Enantioselective Synthesis of Cyclic α ‐Hydroxy Ketones

    Haote Ding, Ling Jiang, Yijia Song, Zhongji Pu, Lirong Yang, Haoran Yu

    Discovered via OpenAlex

  1020. bioRxiv (Cold Spring Harbor Laboratory)

    ESMDisPred: A Structure-Aware CNN-Transformer Architecture for Intrinsically Disordered Protein Prediction

    Md Wasi Ul Kabir, Ayon Dey, Farzeen Nafees, Md Tamjidul Hoque

    Discovered via OpenAlex

  1021. Current Opinion in Structural Biology

    Computational design of intrinsically disordered proteins

    Giulio Tesei, Francesco Pesce, Kresten Lindorff‐Larsen

    Discovered via OpenAlex

  1022. bioRxiv (Cold Spring Harbor Laboratory)

    Benchmarking generative scaffold design methods for peptide engineering in TCR–MHC complexes

    Linhui Xie, Gia-Bao Dam, Yashvi Patel, Lilian Denzler, Yanjun Shao, Ruimin Wang, Étienne Caron, Yoshiaki Yasumizu, David A. Hafler, María Rodríguez Martínez

    Discovered via OpenAlex

  1023. Biomacromolecules

    Molecular Design in l -Glutamic Acid-Based Peptide Assembly Dynamics Driven by Carbodiimide-Fueled Reaction Cycle

    Nagihan Özbek, Xiaoyao Chen, Brigitte A. K. Kriebisch, Adrián Fernández-de-la-Pradilla, Katarzyna Świderek, Job Boekhoven, Beatriu Escuder

    Discovered via OpenAlex

  1024. Blood Advances

    HMB-002: a monovalent antibody that elevates circulating VWF and FVIII levels for treatment of von Willebrand disease

    Mattias Häger, Minka Živkovic, Prafull S. Gandhi, C.E. Rasmussen, Cécile Bonvoisin, Rane A. Harrison, Emil Poulsen, Dana Huskens, Mark Roest, Fortunato Ferrara, Anaïs Naretto, Lionel Renaud, Ole Hvilsted Olsen, Nicolas O. Eskesen, Lars Holten-Andersen, Ruthvik Malladi, Catherine J. Rea, Benny Sørensen, Rolf T. Urbanus, Henrik Ostergaard

    Discovered via OpenAlex

  1025. bioRxiv (Cold Spring Harbor Laboratory)

    High-Affinity Protein Binder Design via Flow Matching and In Silico Maturation

    Qilin Yu, Liangyue Guo, Xiayan Qin, Xikun Huang, Baihui Tian, Hongzhun Wang, Yu Liu, Yunzhi Lang, Di Wang, Zhongkai Shen, Jie Lin, Mingchen Chen

    Discovered via OpenAlex

  1026. Bioinformatics

    GeoGAD: geometry-aware antibody design framework for complementarity-determining region precision engineering

    Songjian Wei, Jinxiong Zhang, Yan Chen, Chunyan Tang, Jiayang Tan

    Discovered via OpenAlex

  1027. Frontiers in Microbiology

    Without safeguards, AI-Biology integration risks accelerating future pandemics

    Dianzhuo Wang, Marian Huot, Zechen Zhang, Kaiyi Jiang, Eugene I. Shakhnovich, Kevin M. Esvelt

    Discovered via OpenAlex

  1028. International Journal of Molecular Sciences

    Hybrid Dual-Context Prompted Cross-Attention Framework with Language Model Guidance for Multi-Label Prediction of Human Off-Target Ligand–Protein Interactions

    Abdullah, Zulaikha Fatima, Muhammad Ateeb Ather, Liliana Chanona-Hernández, José Luis Oropeza Rodríguez

    Discovered via OpenAlex

  1029. Protein Science

    ProteinDJ : A high‐performance and modular protein design pipeline

    Dylan Silke, Julie Iskander, Junqi Pan, Andrew P. Thompson, Anthony T. Papenfuss, Isabelle S. Lucet, Joshua M. Hardy

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.3 RoseTTAFold-based

  1030. Progress in Biophysics and Molecular Biology

    Energy-driven innovations in computational de novo protein engineering

    Kevser Kübra Kırboğa, Ecir Uğur Küçüksille

    Discovered via OpenAlex

  1031. Drug Discovery Today

    Peptide cheminformatics tools: making computational tasks accessible in peptide drug discovery

    Vanessa Erckes, Massina Abderrahmane, Maud Jusot, Christian Steuer, Rodrigo Ochoa

    Discovered via OpenAlex

  1032. Proteins Structure Function and Bioinformatics

    Integration of Evolutionary Analysis With RFdiffusion for De Novo Design of Aggregation‐Resistant Frataxin

    Kevser Kübra Kırboğa, Ecir Uğur Küçüksille

    Discovered via OpenAlex

  1033. Protein Science

    Evaluating zero‐shot prediction of monomeric protein design success by AlphaFold , ESMFold , and ProteinMPNN

    Mario Garcia, Sugyan M. Dixit, Gabriel J. Rocklin

    Discovered via OpenAlex

  1034. Bioinformatics

    De novo protein–ligand design including protein flexibility and conformational adaptation

    Jakob Agamia, Martin Zacharias

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 2. Model-based design · 2.1.1 trRosetta-based

  1035. Cold Spring Harbor Perspectives in Biology

    Guiding Cells with Light and Chemicals: A Toolbox for Dynamic Studies of Cell Migration

    Abhijit Deb Roy, Elmer Rho, Takanari Inoue

    Discovered via OpenAlex

  1036. Journal of Chemical Information and Modeling

    Ab-SELDON: Leveraging Diversity Data for an Efficient Automated Computational Pipeline for Antibody Design

    Jean Vieira Sampaio, Andrielly Henriques Santos-Costa, Aline O. Albuquerque, Júlia S. Souza, Diego S. Almeida, Eduardo Menezes Gaieta, Matheus V. Almeida, G. Sartori, João Hermínio Martins da Silva

    Discovered via OpenAlex

  1037. Sensors and Actuators B Chemical

    Computer-assisted hapten design for developing an ultrasensitive antibody with recognition mechanism analysis and its application in the rapid detection of topramezone

    Shiyun Han, Yiting Wang, Hao Wen, Mingyue Ding, Jiaxu Xiao, Jiacan Wang, Long Li, Linwei Zhang, Xiaoming Pan, Shixiang Wu, Hongfei Yang, Dapeng Peng

    Discovered via OpenAlex

  1038. ACS Infectious Diseases

    One-Step Design of Potent and Nonhemolytic Antimicrobial Peptides by Using a Database-Guided, Nonmachine Learning Approach

    Abraham Fikru Mechesso, Arjun Nair, Guangshun Wang

    Discovered via OpenAlex

  1039. JURNAL BIOLOGI TROPIS

    Prediction of Salmon Inhibitor Peptides For DPP-IV Proteins Using Molecular Docking

    Nahdiyah Vernanda Saputri, Yulanda Antonius

    Discovered via OpenAlex

  1040. International Journal of Surgery

    Inhibition of LONP1 in prostate cancer: bibliometrics-guided target screening and AI-driven antibody design

    Jiawei Pan, Yuan Zhang, Anqi Yang, Linglong JIANG, Yuwei Shen, Yangyang Sun, Jie Zhu, Zhen Chen, Min Fan, Jian Shi

    Discovered via OpenAlex

  1041. arXiv (Cornell University)

    PepEDiff: Zero-Shot Peptide Binder Design via Protein Embedding Diffusion

    Po-Yu Liang, Tibo Duran, Jun Bai

    Discovered via OpenAlex

  1042. Molecular Pharmaceutics

    Nonspecific Cellular Interactions Are a Key Determinant in the Disposition of Fc-Fused Proteins

    Mark A. Bryniarski, Songyu Wang, Aochiu Chen, Brian Coventry, Elif Nihal Korkmaz, Md Tariqul Haque Tuhin, Eunkyung Clare Ko, Devin L. Wakefield, Edward L. LaGory, Hao Wu, Achala N. D. Punchi Hewage, Khue Dang, Marcus Soto, Manuel Ponce, Esperanza Ojeda, Kip P. Conner, Lance J. Stewart, Christine Elaine Tinberg, Ai Ching Lim, David A. Baker, Kevin D. Cook

  1043. Research Square

    Biomolecular condensation using de novo designed globular proteins

    Derek N. Woolfson, Andrey V. Romanyuk, Ragesh Kumar, Stephen Cross, Katarzyna Ożga, Rokas Petrenas, Joel J. Chubb, Jennifer J. McManus

    Discovered via OpenAlex

  1044. ChemRxiv

    A Minimal Computational Workflow for CDR-H3-Inspired Cyclic Peptide Design Targeting an Antibody-Defined Epitope

    Takehito Kojima

    Discovered via OpenAlex

  1045. arXiv (Cornell University)

    AutoBinder Agent: An MCP-Based Agent for End-to-End Protein Binder Design

    Fukang Ge, Jiarui Zhu, Linjie Zhang, Haowen Xiao, Xiangcheng Bao, Fangnan Xie, Danyang Chen, Yanrui Lu, Yuting Wang, Ziqian Guan, Lin Gu, Jinhao Bi, Yingying Zhu

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.4 CNN-based

  1046. Biophysics Reviews

    Deep learning-driven protein structure prediction and design: Key model developments by Nobel laureates and multi-domain applications

    Wanqing Yang, Yanwei Wang, Yang Wang

    Discovered via OpenAlex

  1047. bioRxiv (Cold Spring Harbor Laboratory)

    Protein engineering of a genetically encoded biosensor for wastewater detection of profen NSAIDs

    Zoë Davis, Hao Tian, Ian R. Wheeldon, Sean R. Cutler, Timothy A. Whitehead

    Discovered via OpenAlex

  1048. Zenodo (CERN European Organization for Nuclear Research)

    Chiral Core Alpha-Z2

    Halima Hussain Sayed Hussain

    Discovered via OpenAlex

  1049. bioRxiv (Cold Spring Harbor Laboratory)

    Templating and confining calcium phosphate mineralization within designed protein assemblies

    Le Tracy Yu, Xinqi Li, Harley Pyles, Anjali P. Patni, Andrew J. Borst, Neville P. Bethel, Paul S. Kwon, Connor Weidle, Ryan D. Kibler, Kenneth D. Carr, Yulai Liu, Dongsheng Li, Stanislav Moroz, Hannele Ruohola‐Baker, Shuai Zhang, James J. DeYoreo, David A. Baker

    Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.3 RoseTTAFold-based

  1050. bioRxiv (Cold Spring Harbor Laboratory)

    Origin-1: a generative AI platform for de novo antibody design against novel epitopes

    Simon Levine, Jonathan Edward King, Jacob Stern, David Grayson, Raymond Wang, Rui Yin, Umberto Lupo, Paulina Kulytė, Ryan M. Brand, Tristan Bertin, Robert Pfingsten, Jovan Cejovic, Chelsea Chung, Breanna K. Luton, Andrew Hagemann, Robel Gemechu Haile, Elliot Medina, Pankaj Panwar, Oleksii Dubrovskyi, Chase LaCombe, Zahra Anderson, Derrik Mildh, Scott Benjamin, Joe Kaiser, Joseph Ferron, Marta Sarrico, Alexandria C. Kershner, Apurva Mishra, Kai Ejan, Emily K Marsh, Paul Bringas, Phetsamay Vilaychack, Kyra Chapman, Jacob Ripley, Muttappa Gowda, Kathryn M Collins, Cailen M. McCloskey, Jeremiah S. Joseph, Rylee Ripley, Shaheed A. Abdulhaqq, David Spencer, Tiffany DeVine, Audree Feltner, Michael Guerin, Jeffrey Goby, Jesse Hendricks, Danielle Castillo, Sean McClain, Douglas Ganini, Derek Shpiel, James Mategko, Eder Cruz Garcia, Masoud Zabet‐Moghaddam, John M. Sutton, Zheyuan Guo, Sean M. West, Janani S. Iyer, Amir Shanehsazzadeh

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 4.5 GNN-based · 4.Scaffold to Sequence

  1051. ACS Catalysis

    Computational Redesign and Mechanistic Insights into P450BM3 Enable Regioselective C–H Hydroxylation of Structurally Diverse Steroids

    Qi Ye, Li Zl, Ying Cui, Hongjia Wei, Y. Victoria Zhang, Fan Zhao, Fuju Wang, Yongbo Song, Weizhuo Xu, Jinghai Zhang

    Discovered via OpenAlex

  1052. Animals

    Structural Insights into the Receptor-Binding Domain of Bat Coronavirus HKU5-CoV-2: Implications for Zoonotic Transmission via ACE2

    Manal A. Babaker, Nariman Sindi, Othman Yahya Alyahyawy, Ehssan H. O. Moglad, Mohieldin Elsayid, Thamir Mahmoud Eid, Mohamed Eltaib Elmobark, Hisham N. Altayb

    Discovered via OpenAlex

  1053. Frontiers in Genetics

    Balancing speed and precision in protein folding: a comparison of AlphaFold2, ESMFold, and OmegaFold

    Anna Hýsková, Eva Marsalkova, Petr Šimeček

    Discovered via OpenAlex

  1054. bioRxiv (Cold Spring Harbor Laboratory)

    Designing AI-programmable therapeutics with the EDEN family of foundation models

    Geraldene Munsamy, Gavin Ayres, Carla Greco, Keith Y K Kam, Gus Minto-Cowcher, John St John, Tanggis Bohnuud, Matthew H. Bakalar, William Chow, Robert J. Pecoraro, Marcelo D. T. Torres, Aaron W. Kollasch, Marcus H. Y. Leung, Hassan Sirelkhatim, Francesco Farina, Connor McGinnis, Srijani Sridhar, Daniel Anderson, Francesco Oteri, Ali Taghibakhshi, Jérémie Donà, Tyler C. Shimko, Cedric Steenbeke, Alexandros Papadopoulos, Malcolm Krolick, Fabian C. Spoendlin, Purba Gupta, Sandeep Kumar, Anne M. Bara, Jared Wilbur, Noelia Ferruz, Timur M. Rvachov, Fangping Wang, Hanqun Cao, Hyun-Su Lee, Japan B. Mehta, Raphaël A. G. Chaleil, Valerio Pereno, Sid Potti, Chris Emerson, Roy Tal Dew, Kevin K Yang, Eric Nguyen, Neha Tadimeti, Jillian F. Banfield, Alicia Frame, Emma Bolton, David Ruau, Rory Kelleher, Anthony Beardsworth Costa, Kimberley Powell, César de la Fuente‐Núñez, Glen-Oliver F. Gowers, Oliver Vince, Jonathan D. Finn, Philipp Lorenz

  1055. Acta Pharmacologica Sinica

    Benchmarking co-folding methods to predict the structures of covalent protein–ligand complexes

    Tong-han Zhang, Jin-tao Zhu, Zhi-xian Huang, Juan Xie, J P Pei, Luhua Lai

    Discovered via OpenAlex

  1056. Nature Communications

    Improved protein binder design using β-pairing targeted RFdiffusion

    Isaac Sappington, Martin Toul, David S. Lee, Stephanie A. Robinson, Inna Goreshnik, Clara McCurdy, Tung Ching Chan, Nic Buchholz, Buwei Huang, Dionne K. Vafeados, Mariana Garcia-Sanchez, Nicole Roullier, Matthias Glögl, Christopher J. Kim, Joseph L. Watson, Susana Vázquez Torres, Koen H. G. Verschueren, Kenneth Verstraete, Cynthia S. Hinck, Melisa Benard-Valle, Brian Coventry, Jeremiah Nelson Sims, Green Ahn, Xinru Wang, Andrew P. Hinck, Timothy P. Jenkins, Hannele Ruohola‐Baker, Steven M. Banik, Savvas N. Savvides, David A. Baker

  1057. Communications Biology

    The computationally designed TRI2-2 miniprotein inhibitor protects against multiple SARS-CoV-2 Omicron variants

    Jimin Lee, James Brett Case, Young‐Jun Park, Rashmi Ravichandran, Daniel E. Asarnow, M. Alejandra Tortorici, Jack T Brown, Shilpa Sanapala, Lauren P. Carter, David A. Baker, Michael S. Diamond, David Veesler

  1058. Science and Technology of Advanced Materials Methods

    Multi-objective optimization for designing structurally similar proteins with dissimilar sequences

    Ryo Akiba, Yoshitaka Moriwaki, Ryuichiro Ishitani, Naruki Yoshikawa

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 4.5 GNN-based · 4.Scaffold to Sequence

  1059. Structure

    In silico design of stable single-domain antibodies with high affinity

    Zhongyao Zhang, Rob van der Kant, Iva Marković, David Vizarraga, Teresa Garcia, Katerina Maragkou, Javier Delgado Blanco, Damiano Cianferoni, Gabriele Orlando, Gabriel Cia, Nick Geukens, Carlo Carolis, Alexander N. Volkov, Savvas N. Savvides, Maarten Dewilde, Joost W. H. Schymkowitz, Luis Serrano Pubul, Frédéric Rousseau

    Discovered via OpenAlex

  1060. Advanced Science

    Identification and Characterization of an In Silico Designed Membrane‐Active Peptide with Antiviral Properties

    Pascal von Maltitz, Niek van Hilten, Tatjana Weil, Thunchanok Thummaraj, Jeroen Methorst, Dennis Aschmann, Alexander Kros, Clarissa Read, Jasmina Gačanin, Herre Jelger Risselada, Jan Münch

    Discovered via OpenAlex

  1061. arXiv (Cornell University)

    AntibodyDesignBFN: High-Fidelity Fixed-Backbone Antibody Design via Discrete Bayesian Flow Networks

    Yue Hu, Feng Tao, Junqing Wang, Yingchao Liu

    Discovered via OpenAlex

  1062. arXiv (Cornell University)

    Tensor-DTI: Enhancing Biomolecular Interaction Prediction with Contrastive Embedding Learning

    Manel Gil-Sorribes, Júlia Vilalta-Mor, Isaac Filella-Mercè, Robert Soliva, Álvaro Ciudad, Vı́ctor Guallar, Alexis Molina

    Discovered via OpenAlex

  1063. Science

    Computational design of conformation-biasing mutations to alter protein functions

    Peter E. Cavanagh, Andrew G. Xue, Shizhong A. Dai, Albert Qiang, Tsutomu Matsui, Alice Y. Ting

    Discovered via OpenAlex

  1064. European Journal of Medicinal Chemistry

    Novel dual-functional peptides designed via NanoBiT spike pseudovirus system for real-time monitoring and inhibition of SARS-CoV-2 infection

    Cheng-Han Lin, Hua-Hsin Chiang, Xinrui Yang, Tzu‐Ching Lin, Chin-Hung Tsai, Chih‐Sheng Lin

    Discovered via OpenAlex

  1065. Journal of Computational Design and Engineering

    Systematic evaluation of attention mechanisms in transformer models for De Novo UTS-driven silk protein sequence design

    Hongchul Shin, YUJIN PARK, Junbin Yeom, Sungsoo Na, Taeyoung Yoon

    Discovered via OpenAlex

  1066. Journal of Chemical Information and Modeling

    MolOrgGPT: De Novo Generation via Large Language Models and Reinforcement Learning

    Pablo Varas Pardo, Oscar Toledano, Guillermo Marcos-Ayuso, David Quesada, Nuria Eugenia Campillo

    Discovered via OpenAlex

  1067. Nature Communications

    Deep learning guided design of protease substrates

    Carmen Martin-Alonso, Sarah Alamdari, Tahoura S. Samad, Kevin Yang, Sangeeta N. Bhatia, Ava Amini

  1068. Advanced Intelligent Systems

    AI Guided Protein Design for Next‐Generation Autogenic Engineered Living Materials

    Hoda M Hammad, Anna Duraj‐Thatte

    Discovered via OpenAlex

  1069. bioRxiv (Cold Spring Harbor Laboratory)

    De novo design of metalloproteases for targeted amyloid-β cleavage

    Yannan Qu, Chentong Wang, Hongli Zhu, Yanjun Wang, Longxing Cao

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.2 Diffusion-based

  1070. ChemRxiv

    De Novo Design of Zearalenone Binding Proteins: A Comparison of Tamarind Bio and CARPdock-NISE-Boltz-2 Pipelines for Biosensor Applications

    José Luis Benavides

    Discovered via OpenAlex

  1071. bioRxiv (Cold Spring Harbor Laboratory)

    Protein Language Models and Structure-Based Machine Learning for Prediction of Allosteric Binding Sites in Protein Kinases: An Explainable AI Framework Grounded in Energy Landscape-Encoded Frustration

    Kamila Riedlová, Vít Škrhák, Will Gatlin, Max Ludwick, Lucas Turano, Marián Novotný, David Hoksza, Gennady M. Verkhivker

    Discovered via OpenAlex

  1072. Journal of Agricultural and Food Chemistry

    Advances in the Modification of Enzymatic Properties Based on Protein Engineering Strategies

    Yaoguang Huang, Lingrong Wen, Bao Kang. Yang

    Discovered via OpenAlex

  1073. Gene

    Computational epitope discovery and in silico design of a bispecific antibody model (COMED hook) to block Plasmodium invasion into erythrocytes

    Ahmet Efe Köseoğlu, Nadir Gül, Tuğçe Duran, Cenk Öztürk, Nezih Hekim

    Discovered via OpenAlex

  1074. Science China Life Sciences

    Protein foundation models: a comprehensive survey

    Hao Xu, Liangjie Li, Sangyu Pan, Peng Cheng, Yuxiang Wang, Zhen Rong, Liu Feng, Xingxu Huang, Shengqi Wang, Wenjie Shu

    Discovered via OpenAlex

  1075. Advanced Science

    Dual‐Anchored Clickable Peptide via SPAAC for Gelatinase‐Responsive Antibacterial and Osteogenic Functions on Titanium Implants

    Ru Zhong, Hang Zhou, Chenyang Ye, Lei Chu, Lin Wang, Yingjun Wang

    Discovered via OpenAlex

  1076. OSF Preprints (OSF Preprints)

    Teleological Rendering Engine (TRE) for de novo Protein Design

    Tonatiu Campos-García

    Discovered via OpenAlex

  1077. Proceedings of the National Academy of Sciences

    Design of solubly expressed miniaturized SMART MHCs

    William L. White, Hua Bai, Chun Kim, Kevin M. Jude, Renhua Sun, Laura Guerrero, Xiao Han, Xiaojing Tina Chen, Apala Chaudhuri, Julia E. Bonzanini, Yi Sun, Amarachi E. Onwuka, Nan Wang, Chunyu Wang, Per‐Åke Nygren, Xinting Li, Inna Goreshnik, Aza Allen, Paul M. Levine, Hao Yuan Kueh, Michael C. Jewett, Nikolaos G. Sgourakis, Adnane Achour, K. Christopher García, David A. Baker

  1078. Science Advances

    AI-assisted protein design to rapidly convert antibody sequences to intrabodies targeting diverse peptides and histone modifications

    Gabriel Galindo, Daiki Maejima, Jacob DeRoo, Scott R. Burlingham, Gretchen M. Fixen, Tatsuya Morisaki, Hallie P. Febvre, Ryan Hasbrook, Ning Zhao, Soham Ghosh, E. Handly Mayton, Christopher Davis Snow, Brian J. Geiss, Yasuyuki Ohkawa, Yuko Sato, Hiroshi Kimurâ, Timothy J. Stasevich

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 4.5 GNN-based · 4.Scaffold to Sequence

  1079. Gels

    Ultra-Short Peptide Hydrogels as 3D Bioprinting Materials

    Davina In, Αndroulla N. Miliotou, Panoraia I. Siafaka, Yiannis M. Sarigiannis

    Discovered via OpenAlex

  1080. The Innovation Life

    A comprehensive survey on artificial intelligence for biomolecule design

    Guang Yang, Jianing Li, Qiong Wang, Lianlian Wu, Zhengshan Chen, Peng-Cheng Zhao, Haoyang Wang, Qinglong Wang, Bing Wen, Chao Song, Wenxin Xu, Xiongfei He, Xiao Zhang, Sophia Tsoka, Siu‐Ming Yiu, Fang‐Xiang Wu, Meng Xiao, Shirui Pan, Hui Yu, Song He, Xiaoli Li, Xiaochen Bo, Min Wu, Jian‐Yu Shi

    Discovered via OpenAlex

  1081. The Plant Journal

    Structural dynamics of plant transcription factors and their functional implications

    Shaowen Wu, Wenjie Huang, Wenyang Zhang, Tingquan Wu, Shijuan Yan

    Discovered via OpenAlex

  1082. Protein Engineering Design and Selection

    Bind, catalyze, and quantify: a modern protein and enzyme engineering toolbox of genetically encoded non-canonical amino acids

    Soren C. Spina, Joe Bailey, Blaise R. Kimmel

    Discovered via OpenAlex

  1083. Bioinformatics Advances

    Benchmarking antigen-aware inverse folding methods for antibody design

    Bartosz Janusz, Dawid Chomicz, Sonia Wrobel, Paweł Dudzic, Adithya Polasa, Kyle Martin, Steven J. Darnell, Stephen R. Comeau, Konrad Krawczyk

    Discovered via OpenAlex

  1084. Soft Matter

    Nanopore sequencing with proteins: synchronization and dischronization of molecular dynamics simulations with laboratory and industrial developments

    Zongan Wang, Yuqian Liu, Tao Zeng, Denghui Li, Xiao Shi, Jiawen Zhang, Hao Wang, Liuxin Shi, Jiayuan Zhang, Yinqi Bai, Yuning Zhang, Yuliang Dong

    Discovered via OpenAlex

  1085. Protein Engineering Design and Selection

    Integrating machine learning tools in protein design: a case of MHETase engineering for PET biodeconstruction

    Rommel Santiago Granja‐Travez, Taraka Dale, Ramesh K. Jha

    Discovered via OpenAlex

  1086. IEEE Journal of Biomedical and Health Informatics

    D-Flow : Multi-modality Flow Matching for D-peptide Design

    Fang Wu, Shuting Jin, Xiangru Tang, Junlin Xu, Mark Gerstein, Li Erran Li, James Zou

    Discovered via OpenAlex

  1087. Bioinformatics Advances

    CoV-UniBind: a unified antibody binding database for SARS-CoV-2

    Aryan Bhasin, Francesco Saccon, Callum Canavan, Andrew Robson, Joao Paulo Euko, Alexandra C. Walls, Yunguan Fu

    Discovered via OpenAlex

  1088. SSRN Electronic Journal

    Synthetic Sequence Alignments As Programmable Probes of Conformational Landscapes in Deep Learning Protein Structure Prediction

    Jannik Adrian Gut, Noah Kleinschmidt, Thomas Lemmin

    Discovered via OpenAlex

  1089. Chemical Science

    A platform to design and optimise fluorogenic scFvs for detection of interleukin 33

    Abigail E Reese, Utsa Karmakar, Margherita Restori, Marcela Alejandra Hermoso, George McDonald Church, Erkin Kuru, Marc Vendrell

    Discovered via OpenAlex

  1090. QRB Discovery

    Mass spectrometry integrates protein design into structural biology method development

    Alexander Stevens, Hannah Osterholz, Vsevolod Viliuga, Thibault Vosselman, Surabhi Kokane, Erik G. Marklund, Arne Elofsson, Axel Leppert, Michael Landreh

    Discovered via OpenAlex

  1091. Bioinformatics Advances

    MiLaSol: modeling protein solubility by mixing up multiple protein language models

    Weiwei Lou, Mert Erden, Lenore Cowen

    Discovered via OpenAlex

  1092. Exploring the hydrogen bond enhanced halogen bond as a tool for biomolecular design and engineering

    Margaret G. Walker, Ho, P. Shing, advisor, Christopher Davis Snow, Melo, Marcelo, committee member, Crans, Debbie, committee member

    Discovered via OpenAlex

  1093. The Innovation Drug Discovery

    Physics-informed deep learning: A new paradigm for macromolecular recognition and rational protein design

    Haobo Xie, Hao Wang, Xiaojun Yao, Jinyan Li, Yi Pan, Aiping Lü, Xiangxiang Zeng, Dongsheng Cao, Xiangzheng Fu

    Discovered via OpenAlex

  1094. SSRN Electronic Journal

    In silico Selection of Enzymatic Targets and Chimeric Protein Design for Gliotoxin Inactivation

    Ariadne González-Jiménez, César M. Flores-Ortíz, Nelly Rodríguez‐Peña

    Discovered via OpenAlex

  1095. Research Square

    Polymorph-Independent Resistance to Generative Protein Design Across Five Tau Fibril Folds: A Cross-Tauopathy Benchmark

    Siddhardha Nanda

    Discovered via OpenAlex

  1096. Research Square

    Polymorph-Dependent Success of Generative Protein Design Against Amyloid Fibrils: A Cross-Method Benchmark Including AL Amyloidosis

    Siddhardha Nanda

    Discovered via OpenAlex

  1097. SSRN Electronic Journal

    AI-Guided De Novo Design of Miniprotein Binders against Daboia russelii Acidic Phospholipase A₂ A8CG86: A Multi-Method Framework to Select Candidates before Recombinant Production

    Sujay S. Gaikwad, Shridhar Shukla, Shubhangi Sharma, Chandra Sen, Ashwani Kumar, Ravindra D. Makde

    Discovered via OpenAlex

  1098. Chemical Communications

    Engineering serum stable protein nanosheets with reduced macrophage uptake

    Ishmamul Hoque Sadab, Raka Chakraborty, Kate A. Kunst, Rachel L. Mason, Julie A. Champion

    Discovered via OpenAlex

  1099. Biophysics and Physicobiology

    A thorny path to restore native-level activity in ProteinMPNN-designed NAD+-dependent L-threonine 3-dehydrogenase: Stability gains, activity losses, and recovery strategies

    Aketo Urushibata, Shoryu Fujita, Taichi Chisuga, Shogo Nakano

    Discovered via OpenAlex

  1100. Digital Discovery

    CyclicMPNN: stable cyclic peptide sequence generation

    Andrew C. Powers, Yanapat Janthana, Parisa Hosseinzadeh

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 4.5 GNN-based · 4.Scaffold to Sequence

  1101. ChemistryOpen

    Engineered α‐Helical Peptides with Chelating Agents as Approach to Antibacterial Therapeutics

    Vincenzo Patamia, Erika Saccullo, Michele Larocca, Virginia Fuochi, Salvatore Furnari, Pio Maria Furneri, Agostino Cilibrizzi, Giuseppe Floresta

    Discovered via OpenAlex

  1102. Chemical Science

    3D self-assembly of cyclic peptides into multilayered nanosheets

    Sandra Díaz, Adrian Sanchez-Fernandez, Juan R. Granja, Ignacio Insua, Javier Montenegro

    Discovered via OpenAlex

  1103. Chemical Science

    HFGuidedDesign: de novo design of cyclic peptide binders via structure-guided discrete diffusion

    Hu Haomeng, Renjie Zhu, Zhu Ning, Chengyun Zhang, Tianfeng Shang, Chongyang Li, Jingjing Guo, Xudong Wang, Hongliang Duan

    Discovered via OpenAlex

  1104. RSC Pharmaceutics

    Advanced bispecific antibody design and inhaled biologics; emerging strategies for asthma

    Zeina Kassem, Jenny K.W. Lam, Hanieh Khalili

    Discovered via OpenAlex

  1105. Chemical Science

    Design of permeability-optimized target-binding macrocycles via direct preference optimization

    Heqi Sun, Hong Guan Tan, Yanyi Chu, Jia-Yi Li, Ruixuan Wang, Dongqing Wei

    Discovered via OpenAlex

  1106. Chemical Science

    MAPLE: a machine-learning force-field-native platform for automated reaction modeling and enzyme design

    Xujian Wang, Zeyu Sun, Yilu Zhang, Carlo Asam, Ruzhan Zhu, Wan-Lu Li, Junmei Wang

    Discovered via OpenAlex

  1107. Biomaterials Science

    Host-directed antimicrobial peptide biomaterials for combating Gram-negative bacterial infections

    Muhammad Adil, Muhammad Arshad, Pengfei Zou, Lili Li

    Discovered via OpenAlex

  1108. Figshare

    Additional file 1 of All-atom protein sequence design using discrete diffusion models

    Amelia Villegas-Morcillo, G. Admiraal, Marcel J. T. Reinders, Jana M. Weber

    Discovered via OpenAlex

  1109. ChemistrySelect

    Designing Novel Antiviral Peptides Targeting Dengue NS3 Protease via Long Short‐Term Memory Model, Molecular Docking and Molecular Dynamics Simulations

    Yuan Chongjun, Muhammad Alif Mohammad Latif, Mohd Basyaruddin Abdul Rahman, Bimo Ario Tejo

    Discovered via OpenAlex

  1110. Vita

    AI‐driven antibody design from an antigen sequence

    Pavel G. Sinitcyn, Albert J. R. Heck

    Discovered via OpenAlex

  1111. Advancements in enzyme engineering for industrial biotechnology

    Durgapada Sarkhel

    Discovered via OpenAlex

  1112. Figshare

    Additional file 1 of Combining computer-aided enzyme design and chromosomal integration for plasmid-free biosynthesis of 1,5-pentanediol in Escherichia coli

    Hongyu Deng, Jing Wang, Fei Meng, Chunling Ma, Piwu Li, Wang, Junqing, X Y Wang, Chunhui Zhao, Yan Zhang, Ruiming Wang, Ning Chen

    Discovered via OpenAlex

  1113. PROJECT ZeroFold ║ ║ ║ ║ The Protein Structure Hidden ║ ║ for 70 Years ║ ║ ║ ║ A Universal Target for ║ ║ Neurodegenerative Disease ║ ║

    Peter Nicodem

    Discovered via OpenAlex

  1114. Repository of the Academy's Library (Library of the Hungarian Academy of Sciences)

    Új klonalitásvizsgálat a T-sejt-receptor béta-láncának konstans-1 és -2 régiójára specifikus antitestek használatával T-sejtes lymphoproliferatiókban = Novel T-cell clonality assessment using T-cell receptor beta constant region 1 and 2 antibodies in T-cell lymphoproliferative disorders

    Forró, Barbara, Livia Vida, László Kereskai, Ágnes Lacza, Pál Jáksó

    Discovered via OpenAlex

  1115. Maize Sciences

    PhytoNB: AI-enabled Nanobody Design in Plants

    Tianhao Wu, Zixuan Wang, Anwen Zhao, Fan Xia, Yuxuan Lou, Can Yin, Yanfen Xu, Jianan Zhang, X Wang, Qian CHENG

    Discovered via OpenAlex

  1116. SSRN Electronic Journal

    Resolving Sequence-Structure Misalignment in Antibody Design via Consistency-Aware Flow Matching

    Yuhang Hu, Junwei Hu, Tong Yu, Xiuwen Gong, Jia Wu, Wenbin Hu

    Discovered via OpenAlex

  1117. Pharmacophore

    Diffusion Models for Macrocyclic Peptide Design Using Stability, Permeability, and Binding Constraints

    Patrick O’Connor, Sean Murphy

    Discovered via OpenAlex

  1118. Kobunshi

    Photocontrol of Microtubule Structures Based on Peptide Design

    Hiroshi Inaba

    Discovered via OpenAlex

  1119. Journal of Materials Chemistry B

    Poly(glutamic acid- block -tyrosine) peptides designed for gastrointestinal drug adsorption

    Hunter B. Wood, Joseph T. Dosch, Stella M. Trickett, Juhi Singh, Farin Weinger, Gerald Wang, Dazhe Cao, Stefanie Arlene Sydlik

    Discovered via OpenAlex

  1120. In Silico Research in Biomedicine

    Insights into the interactions and molecular dynamics of potent inhibitory peptides against BLEG-1 B3 metallo-β-lactamase through molecular dynamics simulations

    Shaw Xian Au, Yahaya Mohd Normi

    Discovered via OpenAlex

  1121. Journal of Materials Chemistry B

    Programmable short peptide condensates with intrinsic enzyme-like activity

    Hao Han, Siyu Song, Siyu Song, Tsvetomir Ivanov, Dongdong Zhou, Hao Su, Shoupeng Cao

    Discovered via OpenAlex

  1122. IEEE Journal of Biomedical and Health Informatics

    Multi-Property Optimization of Antimicrobial Peptides Using Reinforcement Learning and Conditional Independence Regularization

    Liwei Xiao, Zhiqiang Liang, Lijuan Wang, X Liu, Qiyu Wang, Yaozhen Liang, Junjie Chen

    Discovered via OpenAlex

  1123. SSRN Electronic Journal

    Gen-YSD: An Experiment-Aware Generative AI Pipeline for Closing the Sim-to-Real Gap in Pan-Hantavirus Antibody Design

    Bala Bhaskar Kumbhagiri

    Discovered via OpenAlex

  1124. SSRN Electronic Journal

    De Novo Design of High-Affinity Antibody Using an Antigen-Aware Diffusion Framework

    Nayereh Seyed Afiuny, Amir Lakizadeh

    Discovered via OpenAlex

  1125. Chemical Science

    Computational data as the fuel for AI in chemistry

    Ross James Urquhart, Tell Tuttle

    Discovered via OpenAlex

  1126. Research Square

    Disclosed and Undisclosed GPU Hardware Exclusion Across the Modern Protein Structure Prediction and Design Toolchain: A Compute-Accessibility Audit

    Siddhardha Nanda

    Discovered via OpenAlex

  1127. RSC Medicinal Chemistry

    Benchmarking AI-driven protocols for cyclic peptide conformer prediction and ranking

    Jovan Damjanovic, Rodrigo Ochoa

    Discovered via OpenAlex

  1128. The Innovation Drug Discovery

    The evolution of computation-driven paradigms in targeted peptide drug design: From predictive modeling to generative AI and clinical translation

    Wenjing Hu, Yuan Sun, Ting Li, Mark Williamson, Xiaoying Hu, Maolin Wang

    Discovered via OpenAlex

  1129. IEEE Journal of Biomedical and Health Informatics

    GeoCTP: Structure-aware Prediction of Multifunctional Cancer Therapy Peptides via Graph Transformer and Contrastive Learning

    Jiahui Guan, Lantian Yao, Peilin Xie, Zhihao Zhao, Dian Meng, Zimeng Chen, Tzong-Yi Lee, Ying‐Chih Chiang, Junwen Wang

    Discovered via OpenAlex

  1130. Daedalus

    AI as the Ultimate Tool for Science: A Conversation with Demis Hassabis

    Demis Hassabis, James Manyika

    Discovered via OpenAlex

  1131. Protein Engineering Design and Selection

    Combining bacterial display and protein language models to engineer a CD69-binding affibody for molecular imaging of immune activation

    Hugo Olsson, Cornelia Westerberg, Jonas Persson, Lina Löfstrand, Olle Korsgren, Olof Eriksson, Stefan Ståhl, John Löfblom

    Discovered via OpenAlex

  1132. SSRN Electronic Journal

    A Multi-View Contrastive Graph Learning Framework for RNA–Protein Interaction Prediction

    Neha Kumari, Kavinder Singh, Néel Sarovar Bhavesh, Yasha Hasija

    Discovered via OpenAlex

  1133. Deep Learning–Driven De Novo Design of Antimicrobial Peptides Active in Human Serum: A Systematic Review of Architectures, Serum Conditions, and Activity Retention

    Sweety Akter, Mustafa Abrar Zaman

    Discovered via OpenAlex

  1134. IPSJ Transactions on Bioinformatics

    Reinforcement Learning Based Design of Protein-binding RNA Sequences

    Ayuka Ishii, Manato Akiyama, Yasubumi Sakakibara

    Discovered via OpenAlex

  1135. Advances in Bioscience and Biotechnology

    Generative Artificial Intelligence in Biology and Medicine

    Philip de Melo

    Discovered via OpenAlex

  1136. Kobunshi

    Advancing High-Performance Protein Engineering Beyond Conventional Knowledge: From Supervised Machine Learning to Protein Language Models

    Mitsuo Umetsu

    Discovered via OpenAlex

  1137. SSRN Electronic Journal

    CodonOptimus: A Ribosome-Profiling-Supervised Foundation Model For Codon Optimisation and Recombinant Protein Production in Microbial Cell Factories

    Munish Puri, Rajesh Sathyamoorthy

    Discovered via OpenAlex

  1138. Emergent-scale prediction of molecular properties with chemically-informed neural networks

    Kumar, Sabari Nath, author, Kim, Seonah, advisor, Sambur, Justin, committee member, St. John, Peter, committee member, Shrideep Pallickara

    Discovered via OpenAlex

  1139. Method-, conformer-count-, and solvent-robust ranking of natural-product screening corpora via xtb semi-empirical quantum chemistry: a multi-axis robustness benchmark

    Han Cheong Woo

    Discovered via OpenAlex

  1140. Cost-Aware Multi-Fidelity Bayesian Optimization with Runtime-Gated Cascading Tiers for Autonomous in silico Dermatology Discovery

    Han Cheong Woo

    Discovered via OpenAlex

  1141. Endocrinologia & Diabetes Clínica e Experimental

    in silico design of a multimodal trimeric peptide candidate predicted to simultaneously target glycemic control, autoimmunity, and pancreatic ß-cell regeneration in type 1 diabetes

    Luís Jesuino de Ol iveira Andrade5, Luís Matos de Oliveira

    Discovered via OpenAlex

  1142. SSRN Electronic Journal

    De Novo-Designed Fluorescent Binding Protein-Based Screening of a High Tannase-producing Klebsiella Strain from Daqu

    Ziqi Liang, Guanhua Jiao, Dan Li, Sheng Gao, Meng Wang, Jing Hu, Yizhen Lu, Jinkai Dong, Xiaoning Zhang, Junwei Zeng, Junqing Wang, Ruiming Wang

    Discovered via OpenAlex

  1143. AIMS Biophysics

    AI-driven prediction of 14-3-3–intrinsically disordered protein interactions: From SLiM discovery to structural modeling of dynamic binding interfaces

    Sergio Müller, Instituto de Histología y Embriología de Mendoza (IHEM), Universidad Nacional de Cuyo, CONICET, Mendoza, Argentina, Ignacio Moreno Guerci, Diego M. Bustos, Facultad de Ciencias Exactas y Naturales, UNCUYO, Mendoza, Argentina

    Discovered via OpenAlex

  1144. Journal of Biomolecular Structure and Dynamics

    Dynamics-informed RFdiffusion for de novo design of binders against the KRAS conformational ensemble

    Kevser Kübra Kırboğa

    Discovered via OpenAlex

  1145. Nature Machine Intelligence

    Assessing the potential of deep learning for protein–ligand docking

    Alex Morehead, Nabin Giri, Jian Liu, Pawan Neupane, Jianlin Cheng

    Discovered via OpenAlex

  1146. Crystals

    Rational Engineering in Protein Crystallization: Integrating Physicochemical Principles, Molecular Scaffolds, and Computational Design

    S. ITO, Tatsuya Nishino

    Discovered via OpenAlex

  1147. arXiv (Cornell University)

    SeedProteo: Accurate De Novo All-Atom Design of Protein Binders

    Qu Wei, Ma Yiming, Ye Fei, Lu Chan, Zhou Yi, Zhang Kexin, Wang Lan, Gui Minrui, Gu Quanquan

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.2 Diffusion-based

  1148. ChemRxiv

    Curiosity-driven de novo protein design via polymerized amyloids

    Tianyi Jin, Jacob Sass, Wenhao Gao, Connor W. Coley, Alfredo Alexander‐Katz

    Discovered via OpenAlex

  1149. ACS Applied Bio Materials

    Self-Assembled Hydrogel from Pyrene-Modified Peptide as 3D Matrices for Neuronal Cell

    Devi Wahyuningtyas, Ya-Ting Yu, Chin-Yun Hsieh, Yung-An Huang, Ruei‐Yu He, Tzu-Hung Teng, Bryan Po-Wen Chen, Jung-Ren Huang, David T. Wu, Joseph Jen‐Tse Huang

    Discovered via OpenAlex

  1150. Synthetic and Systems Biotechnology

    Engineering a broad-spectrum glucose oxidase via substrate channel and linker design for enhanced lignocellulose bioconversion

    Yong Feng, Xihua Chen, Zeyang Li, Zhong Wen Ni, Zhengfen Wu, Zhongjian Guo, Fubao Fuelbiol Sun, Huiqing Chen, Huayou Chen

    Discovered via OpenAlex

  1151. The Journal of Chemical Physics

    A patchy-particle three-dimensional octagonal quasicrystal

    Akie Kowaguchi, Savan Mehta, Jonathan P. K. Doye, Eva G. Noya

    Discovered via OpenAlex

  1152. Zenodo (CERN European Organization for Nuclear Research)

    Adaptive Protein Design and Optimization (APDO): An Energy-Driven Framework for Protein Structure Optimization

    PRABIN KUMAR

    Discovered via OpenAlex

  1153. bioRxiv (Cold Spring Harbor Laboratory)

    Iterative Epitope Expansion Enables Structure-Guided de novo Design of IgE-Binding Miniproteins Targeting the Fc ε RI Interface

    Ido Calman, Hamed Shaykhalishahi, Puwanat Sangkhapreecha, Sharrol T. Bachas

    Discovered via OpenAlex

  1154. Biotechnology Advances

    Geometric deep learning assists protein engineering. Opportunities and Challenges

    Julián Alfonso García - Vinuesa, Jorge Alejandro Rojas, Nicole Soto-García, Nicolás Martínez, Diego Álvarez-Saravia, Roberto Uribe-Paredes, Mehdi D. Davari, Carlos Conca, Juan A. Asenjo, David Medina-Ortiz

    Discovered via OpenAlex

  1155. bioRxiv (Cold Spring Harbor Laboratory)

    To Predict is to Design: Unlocking Generative Capabilities in All-Atom Structure Predictors via Geometric Score Distillation

    Yuxuan Li, Yeyu Su, Yanbo Jing, Tao Liu

    Discovered via OpenAlex

  1156. Chemical Communications

    Supramolecular self-assembled peptide scaffolds for fluorescence enhancement and delayed emission

    Sowbhick Patra, Goutam Ghosh

    Discovered via OpenAlex

  1157. arXiv (Cornell University)

    DuaDeep-SeqAffinity: Dual-Branch Deep Learning for Tri-Stream Sequence-Based Antibody--Antigen Affinity Prediction

    Aicha Boutorh, Soumia Bouyahiaoui, Manel Kara Laouar, Sara Belhadj, Nour El Yakine Guendouz, Asma Boutorh

    Discovered via OpenAlex

  1158. bioRxiv (Cold Spring Harbor Laboratory)

    Clearing the whey: Efficient inhibition and removal of chymosin from whey by de novo designed protein-based inhibitors

    Darian Stephan Wolff, Casper de Lichtenberg, Josefine Gjelstrup Larsen, Carsten Andersen, Timothy P. Jenkins

    Discovered via OpenAlex

  1159. bioRxiv (Cold Spring Harbor Laboratory)

    B-PPI: A Cross-Attention Model for Large-Scale Bacterial Protein-Protein Interaction Prediction

    Chen Agassy, Bruria Samuel, Shahar Mayo, Asaf Zorea, David E Burstein

    Discovered via OpenAlex

  1160. bioRxiv (Cold Spring Harbor Laboratory)

    FlashBind: Towards Accurate and Efficient Structure-based Virtual Screening

    Songlin Jiang, Yifan Chen, Aarti Krishnan, Yu Zhang, Wengong Jin

    Discovered via OpenAlex

  1161. Nature Communications

    Stable de novo protein design via joint conformational landscape and sequence optimization

    Yehlin Cho, Justas Dauparas, Kotaro Tsuboyama, Gabriel J. Rocklin, Sergey Ovchinnikov

  1162. bioRxiv (Cold Spring Harbor Laboratory)

    Mechanistic Interpretability of Fine-Tuned Protein Language Models for Nanobody Thermostability Prediction

    Taihei Murakami, Yuki Hashidate, Yasuhiro Matsunaga

    Discovered via OpenAlex

  1163. Materials Advances

    Self-assembling protein cages: from coiled-coil module to machine learning-driven de novo design of next-generation biomaterials

    Arvind Kumar Gupta, Hana Esih, Helena Gradišar, Roman Jerala

    Discovered via OpenAlex

  1164. bioRxiv (Cold Spring Harbor Laboratory)

    Computational design and experimental characterization of mini-protein binders targeting Nipah, Langya and Measles virus receptor-binding domains

    D. L. RIEGER, Carolin Rüdiger, Antonia Sophia Peter, Phillip Schlegel, Anna Nobis, Hannes Junker, Lena Kiesewetter, Max Beining, Lorenz Beckmann, Johannes Klier, Nichakorn Pipatpadungsin, Robert Stass, Thomas A. Bowden, Sandra Diederich, Jens Meiler, Clara T. Schoeder

    Discovered via OpenAlex

  1165. bioRxiv (Cold Spring Harbor Laboratory)

    De novo design of protein binders that target DELE1 to inhibit the mitochondrial stress response

    Rui Yang, Kaiyuan Zheng, McGuire Metts, Yiluo Wang, Danyan YIN, Kevin P. Li, Agnieszka A. Prazmowska, David F. Kashatus, Brian A. Kuhlman, Jie Yang

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.3 RoseTTAFold-based

  1166. International Journal of Peptide Research and Therapeutics

    Peptide-Based Cancer Vaccines: Engineering Immune Precision Against Tumor Evolution

    Sivaraj Mehnath

    Discovered via OpenAlex

  1167. Physical Chemistry Chemical Physics

    LMProtein: a protein language model based framework for protein structural property prediction

    Yongna Yuan, Hui Luo, Yaojie Tian

    Discovered via OpenAlex

  1168. bioRxiv (Cold Spring Harbor Laboratory)

    Combinatorial Protein Language Model–Guided Engineering of TEV Protease for Enhanced Stability and Production

    Tek Hyung Lee, Songming Liu, Yifan Li, Trang Nguyen, Zhaoren He, Sagar D. Khare, Li zu yi

    Discovered via OpenAlex

  1169. Protein Engineering Design and Selection

    Experimental analyses of RFdiffusion designed Miniproteins for binding to SARS-CoV-2 nucleocapsid protein

    Zeenat Khakerwala, Ashwani Kumar, Sujay S. Gaikwad, T. Barik, Shweta Singh, Gagan D. Gupta, Ravindra D. Makde

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.3 RoseTTAFold-based

  1170. bioRxiv (Cold Spring Harbor Laboratory)

    De novo design of protein nanoparticles with integrated functional motifs

    Cyrus M. Haas, Sanela Rankovic, Hanul K Lewis, Kenneth D. Carr, Connor Weidle, Sophie S Gerdes, L. Nuss, Felicitas Ruiz, Syed Moiz, Maggie Fiorelli, Emily Grey, Jackson McGowan, N. Pavan Kumar, Adrian Creanga, Alex Kang, Hannah Nguyen, Yanqing Wang, Banumathi Sankaran, Annie M. Dosey, Rashmi Ravichandran, Asim K. Bera, Elizabeth M. Leaf, Cole A. DeForest, Masaru Kanekiyo, Andrew J. Borst, Neil P. King

    Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.3 RoseTTAFold-based

  1171. bioRxiv (Cold Spring Harbor Laboratory)

    De novo designed bifunctional proteins for targeted protein degradation

    Bram Mylemans, Bogusława Korona, Amanda M. Acevedo‐Jake, Ailsa MacRae, Thomas A. Edwards, Danny T. C. Huang, Andrew John Wilson, Laura S. Itzhaki, Derek N. Woolfson

    Discovered via OpenAlex

  1172. ACS Omega

    A Multiepitope Protein Based on Selected Synthetic Peptides Enables Effective Serological Screening of Exposure to Mycobacterium leprae

    Augusto César Parreiras de Jesus, Tatyane Martins Cirilo, José Bryan da Rocha Rihs, Tânia Mara Pinto Dabés Guimarães, Hayana Ramos Lima, Sebastião Rodrigo Ferreira, Rocio Arreguin-Campos, Cristiane Alves da Silva Menezes, Lilian Lacerda Bueno, Bart van Grinsven, Thomas Jan Cleij, Ana Laura Grossi de Oliveira, Ricardo Toshio Fujiwara

    Discovered via OpenAlex

  1173. Quantitative Biology

    Protein design and RNA design: Perspectives

    Xi Chen, Xu Dai, Peilong Lu

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 1. Reviews · 1.1 De novo protein design

  1174. Zenodo (CERN European Organization for Nuclear Research)

    Computational Protein Design – Test report and proposal

    PRABIN KUMAR

    Discovered via OpenAlex

  1175. Molecules

    AI-Driven Enzyme Engineering: Emerging Models and Next-Generation Biotechnological Applications

    Mohd Faheem Khan, Mohd. Tasleem Khan

    Discovered via OpenAlex

  1176. Biotechnology Advances

    From traditional to AI-driven: The evolution of intelligent enzyme engineering for biocatalysis

    Feifei Lv, Jiaxing Zhang, Shengping You, Wei Qi

    Discovered via OpenAlex

  1177. International Microbiology

    Microbial engineering for sustainable microplastic biodegradation: from enzyme redesign to synthetic consortia

    Simran, Ghanima Amin, Md Golam Kabir

    Discovered via OpenAlex

  1178. bioRxiv (Cold Spring Harbor Laboratory)

    Evolutionary Decoding of the Bacillus subtilis Secretome: Insights from Pan-Genomics and Deep Learning

    Chong Peng, Chengwu Yuan, Linhao Meng, Yuying Chen, Shuang Wen, Fuping Lu, Yihan Liu

    Discovered via OpenAlex

  1179. Journal of Chemical Information and Modeling

    A Comparative Study of Deep Learning and Classical Modeling Approaches for Protein–Ligand Binding Pose and Affinity Prediction in Coronavirus Main Proteases

    Yue Liu, Haocheng Tang, Taoyu Niu, Junmei Wang

    Discovered via OpenAlex

  1180. Bioorganic & Medicinal Chemistry Letters

    AI-guided design of cyclic peptide binders targeting TREM2 using CycleRFdiffusion and experimental validation

    Sungwoo Cho, Renjie Zhu, Katarzyna Kuncewicz, Hongliang Duan, Moustafa Tarek Gabr

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.3 RoseTTAFold-based

  1181. Nature Communications

    Generalizable and scalable protein stability prediction with rewired protein generative models

    Ziang Li, Yunan Luo

    Discovered via OpenAlex

  1182. Zenodo (CERN European Organization for Nuclear Research)

    Computational Protein Design – Validation & Benchmarking Update

    PRABIN KUMAR

    Discovered via OpenAlex

  1183. Antiviral Research

    Single-shot design of a cyclic peptide inhibitor of HIV membrane fusion

    Diandra Daumiller, Federica Giammarino, Qiuzhen Li, Anders B. Sönnerborg, Rafael Ceña Diez, Patrick Bryant

    Discovered via OpenAlex

  1184. MedScien

    Transformation of Protein Design: From Traditional Approaches to AI-Driven Precision Engineering

    Xin Fang

    Discovered via OpenAlex

  1185. IEEE Computer Architecture Letters

    Understanding the Performance Behaviors of End-to-End Protein Design Pipelines on GPUs

    Jinwoo Hwang, Yeongmin Hwang, Tadiwos Meaza, Hyeonbin Bae, Jongse Park

    Discovered via OpenAlex

  1186. arXiv (Cornell University)

    Structure-Aware Antibody Design with Affinity-Optimized Inverse Folding

    Xinyan Zhao, Tang Yi-Ching, Rivaaj Monsia, Victor Cantu, Ashwin Kumar Ramesh, Xiaozhong Liu, Zhiqiang An, Xiaoqian Jiang, Yejin Kim

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 4.7 Transformer-based · 4.Scaffold to Sequence

  1187. Foods

    Glucosinolate–Myrosinase Formulations for Adult Obesity: Towards Next Generation of Bioactive Therapies

    Concepción Medrano‐Padial, Cassidy Bo Harris, Verónica Mellado-Romero, Raúl Domínguez‐Perles, Diego A. Moreno

    Discovered via OpenAlex

  1188. Journal of Molecular Biology

    Evolution and design shape protein dynamics in LOV domains – spanning picoseconds to days

    Raoul E. Herzog, Isabelle F. Harvey-Seutcheu, Philipp Janke, Wenzhao Dai, Paul M. Fischer, Peter Hamm, Philipp J. Heckmeier

    Discovered via OpenAlex

  1189. Bioinformatics

    SurfFold: a unified model for protein inverse folding by integrating surface and structural information

    Darong Li, Lian Shen, Meijia Song, Deyi Li, Juan Liu, Xiangrong Liu

    Discovered via OpenAlex

  1190. Nature Chemical Biology

    Harnessing advances in artificial intelligence for protein design

    Russell Johnson

    Discovered via OpenAlex

  1191. bioRxiv (Cold Spring Harbor Laboratory)

    LoMuS: Low-Rank Adaptation with Multimodal Representations Improves Protein Stability Prediction

    Samuel Infante Trillos, Akash Singh, Anowarul Kabir

    Discovered via OpenAlex

  1192. bioRxiv (Cold Spring Harbor Laboratory)

    De novo designed protein enables precise epitope-level control of Gremlin-1 antagonism

    Bunia I. Adsersen, Cecilie M. Møller-Jensen, Christian P. Jacobsen, Tanja Domeyer, Johannes R. Loeffler, Monica L. Fernandez-Quintero, Iacopo Tomberli, Astrid B. Jensen, Mikkel S. Jakobsen, Sandhya Bangaru, Andrew Ward, Esperanza Rivera‐de‐Torre, Stefán B. Gunnarsson, Andreas Hald, Timothy P. Jenkins

    Discovered via OpenAlex

  1193. npj Viruses

    VHH antibody loop guides design of a synthetic macrocyclic peptide that potently blocks influenza virus membrane fusion

    Rameshwar U. Kadam, Jarek Juraszek, Boerries Brandenburg, Divita Garg, Xueyong Zhu, Mandy A. C. Jongeneelen, Wim B. G. Schepens, Bart Stoops, Jan Vermond, Wouter Goutier, Chan Tang, Sven Blokland, Ronald Vogels, Robert H. E. Friesen, Maria J. P. van Dongen, Ian A. Wilson

    Discovered via OpenAlex

  1194. International Journal of Biological Macromolecules

    Electrochemical techniques in protein engineering: Innovations in redox-active protein design and electron transfer mechanisms

    Nagarjuna Prakash Dalbanjan, Karuna Korgaonkar, Arihant Jayawant Kadapure, Maruti J. Gurav, Vishwanath B. Chachadi, S.K. Praveen Kumar

    Discovered via OpenAlex

  1195. arXiv (Cornell University)

    HD-Prot: A Protein Language Model for Joint Sequence-Structure Modeling with Continuous Structure Tokens

    Zhou, Yi, Qu, Haohao, Liu, Yunqing, Lin, Shanru, Song, Le, Fan, Wenqi

    Discovered via OpenAlex

  1196. International Journal of Biological Macromolecules

    Development of a highly functional thermostable D-amino acid oxidase for efficient L-phosphinothricin biosynthesis using ProteinMPNN-guided engineering

    Kai Yang, Yueshan Huang, Liyi Yao, Bin Huang, Weimin Zeng, Jin Huang

    Discovered via OpenAlex

  1197. Meta-Learning for Binding Affinity Prediction in Fixed-Target DARPin Engineering

    Md Raiyan Chowdhury, Michael Woolley, Jian Tao, Zhilei Chen, Xiaoning Qian

    Discovered via OpenAlex

  1198. bioRxiv (Cold Spring Harbor Laboratory)

    Computational reconstruction of Tyrannosaurus rex collagen for biomanufacturing of paleo-inspired biomaterials with tuneable stiffness

    T Mitchell, Ernst Jurgen Wolvetang

    Discovered via OpenAlex

  1199. Chemistry Letters

    Computational redesign of the heme acquisition protein HasA for enhanced thermostability while retaining its ability to bind synthetic metalloporphyrins

    Sukyeong Kim, Aketo Urushibata, Nanako Yamauchi, Hiroshi Sugimoto, Shogo Nakano, Osami Shoji

    Discovered via OpenAlex

  1200. aBIOTECH

    Deep learning–driven protein binder design for crop improvement

    Muhammad Salman Iqbal, Revocatus Bahitwa, Abdul Ali Azam, Hui Xu, Hai Wang

    Discovered via OpenAlex

  1201. bioRxiv (Cold Spring Harbor Laboratory)

    Sequence and structural determinants of efficacious de novo chimeric antigen receptors

    Arthur Chow, Hoyin Chu, Ruofan Li, Benan N. Nalbant, Abdul Vehab Dozic, Laura C. Kida, Caleb A. Lareau

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 2. Model-based design · 2.1.1 trRosetta-based

  1202. Polymer Degradation and Stability

    Inspired by the catalytic properties of biological enzymes: Design of bifunctional catalytic flame retardants for enhanced polyurethane flame retardancy

    Xingyao Li, Kangcheng Xu, Lin Wang, Yulu Zhang, Zhishuai Geng, Xangmei Li, Jiyu He, Rongjie Yang

    Discovered via OpenAlex

  1203. Journal of Biological Chemistry

    A bispecific antibody designed to act as a NRP2/PLXNA1 agonist mimics anticancer activity of SEMA3F

    Hong-Lei Tian, Chun Po Fung, Luke Burman, Yeeting Esther Chong, Changdong Liu, Yanyan Geng, Lam Yang, Man Wai Chow, Yingyi Zhang, Kwok Wa Hugo Ho, Guang Zhu, Zhenguo Wu, Xiang‐Lei Yang, Zhiwen Xu, Leslie A. Nangle

    Discovered via OpenAlex

  1204. Process Biochemistry

    SoluBat: A bidirectional mamba framework for high-throughput protein solubility prediction in bioprocess optimization

    Liguo Wu, C.H. Zhang, Zijian Hu, Xurong Wang, Hongrong Liu, Bin Zhu

    Discovered via OpenAlex

  1205. Nature Communications

    Structure-based design of macrocyclic peptides to generate functional antibodies against G protein-coupled receptors

    Marie-Édith Nepveu-Traversy, Malihe Hassanzadeh, Laurent Bruneau‐Cossette, Élie Besserer‐Offroy, Rebecca L. Brouillette, Sandra Morissette, Hassan Traboulsi, Karyn Kirby, Alexandre Murza, Jean‐Michel Longpré, Billy Breton, Fernand‐Pierre Gendron, Simon Gaudreau, Pierre‐Luc Boudreault, Philippe Sarret

    Discovered via OpenAlex

  1206. Journal of Controlled Release

    A dual-responsive AI-designed peptide P9-conjugate disrupts E6–E6AP Interface to restore p53 and suppress HPV16-driven cervical cancer

    Yue Hua, Yi Xu, Jiale Wan, Yiqing Fan, Xi Zeng, Hai Qian, Yang Shen

    Discovered via OpenAlex

  1207. Theoretical and Natural Science

    Applications of AlphaFold in the Medical Field

    Zhi Lin Tan

    Discovered via OpenAlex

  1208. arXiv (Cornell University)

    Self Distillation Fine-Tuning of Protein Language Models Improves Versatility in Protein Design

    Amin Tavakoli, Murugan, Raswanth, Ozan Gökdemir, Arvind Ramanathan, Frances H. Arnold, Animashree Anandkumar

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 5.4 Transformer-based · 5.Function to Sequence

  1209. Research Square

    Rapid Assessment of Chemical Complementarity of Ligands for Protein Design

    Derek N. Woolfson, Rokas Petrenas, Katarzyna Ożga, Joel Chubb, Andrey Romanyuk, Jennifer J. McManus, Graham J. Leggett, Nigel Shaun Scrutton, Tom Oliver

    Discovered via OpenAlex

  1210. Illinois Digital Environment for Access to Learning and Scholarship (University of Illinois at Urbana-Champaign)

    AI Guided Mutation Prediction and Vaccine Development Using Inverse Folding

    Muhammad A. Ali

    Discovered via OpenAlex

  1211. Nature Communications

    De novo design of epitope-specific antibodies via a structure-driven computational workflow

    Fandi Wu, Yu Shan Zhao, Jiaxiang Wu, Biaobin Jiang, Bing He, Long-Kai Huang, Chenchen Qin, Yang Xiao, Fan Yang, Rubo Wang, Ningqiao Huang, Huaxian Jia, Yuyi Liu, Houtim Lai, Tingyang Xu, Fang Wang, Zihan Wu, Yidong Song, Shaoning Li, Wei Liu, Yu Rong, Peilin Zhao, Jianhua Yao

    Discovered via OpenAlex

  1212. Green Synthesis and Catalysis

    Intelligent enzyme design and hybrid catalytic systems: Driving innovation in biocatalysis

    Ge Qu, Fangrui Zhong, Jian Feng Xu, Xiaoqiang Huang, Zhoutong Sun

    Discovered via OpenAlex

  1213. bioRxiv (Cold Spring Harbor Laboratory)

    Engineering a Covalent Linkage into a Dimeric De Novo Enzyme Reveals a Novel Life-Sustaining Mechanism

    Guanyu Liao, Sha Tao, Mina Nagahara, Kodai Kurihara, Koji Umezawa, Ryoichi Arai, Michael H. Hecht

    Discovered via OpenAlex

  1214. arXiv (Cornell University)

    De novo generation of functional terpene synthases using TpsGPT

    Ramanathan, Hamsini, Bushuiev, Roman, Soldát, Matouš, Kohout, Jirí, Téo Hebra, Smith, Joshua David, Josef Šivic, Tomáš Pluskal

    Discovered via OpenAlex

  1215. Green Synthesis and Catalysis

    Advances in benzaldehyde lyase-catalyzed biotransformations: From enzyme engineering to industrial applications

    Zhiyun Li, Junwei Huang, Bin Chen, Shilong Dou, Xiaoxia Liu, Wei Zhu, Zhiran Ju, Fen‐Er Chen

    Discovered via OpenAlex

  1216. Journal of Chemical Education

    Cohort-Based Learning of Computational Protein Design: Engineering a Helical Protein To Improve Its Stability

    Beas Mukherjee, Soumya De

    Discovered via OpenAlex

  1217. Journal of Chemical Information and Modeling

    AcidProNet: Acidophilic Protein Classification via DCGAN-GP-Based Data Augmentation and Parameter-Shared Mixture-of-Experts Transformer

    Jiaxing Song, Aoyun Geng, Qianmao Wen, Junlin Xu, Yajie Meng, Feifei Cui, Quan Zou, Leyi Wei, Zilong Zhang

    Discovered via OpenAlex

  1218. arXiv (Cornell University)

    On fine-tuning Boltz-2 for protein-protein affinity prediction

    King, James, Cornwall, Lewis, Nica, Andrei Cristian, Day, James, Sim, Aaron, Dalchau, Neil, Wollman, Lilly, Meyers, Joshua

    Discovered via OpenAlex

  1219. Zenodo (CERN European Organization for Nuclear Research)

    DPO: Precision Control for Aligned Generative Models

    Revista, Zen, IA, 10

    Discovered via OpenAlex

  1220. bioRxiv (Cold Spring Harbor Laboratory)

    Energetic Constraints in the Enzymatic Depolymerization of Crystalline PET

    Ania Di Pede-Mattatelli, Miguel A. Maria‐Solano, Oleksandr Haisha, Francesco Colizzi

    Discovered via OpenAlex

  1221. Nucleic Acids Research

    Enzyme Engineering Database (EnzEngDB): a platform for sharing and interpreting sequence–function relationships across protein engineering campaigns

    Yueming Long, Fatemeh Abbasinejad, Francesca-Zhoufan Li, Pierre Reinprecht, Bruce J. Wittmann, Jennifer L. Kennemur, Hayden M. Carder, Jason Yang, Théophile Lambert, Ryen L. O’Meara, Lukas Radtke, Ziyang Qin, Sabine Brinkmann‐Chen, Frances H. Arnold, Ariane Mora

    Discovered via OpenAlex

  1222. ACS Synthetic Biology

    Design of a Labile RNase A Using Protein Language Models

    Gabriel Ong, Kiat Whye Kong, Si En Poh, Fong Tian Wong, Yiqi Seow, Winston Lian Chye Koh

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 7. Other tasks · 7.1 Effects of mutation & Fitness Landscape

  1223. Communications Chemistry

    Designing novel solenoid proteins with in silico evolution

    Daniella Pretorius, Georgi I. Nikov, Kono Washio, Steve-William Florent, Henry N. Taunt, Sergey Ovchinnikov, James W. Murray

    Curated by Papers for Protein Design Using Deep Learning · 2. Model-based design · 2.1.1 trRosetta-based

  1224. Synthetic and Systems Biotechnology

    Transfer learning with pre-trained language models for protein expression level prediction in Escherichia coli

    Chunhe Yang, Yuling Zhao, Ruoyu Wang, Haoran Li, Xiaoping Liao, Hongwu Ma

    Discovered via OpenAlex

  1225. Acta Biochimica et Biophysica Sinica

    Bioinformatics classification of the MgtE Mg2 + channel and de novo protein design for the stabilization of its novel subclass

    Zhixuan Zhao, Kimiho Omae, Wataru Iwasaki, Ziyi Zhang, Fazhi Pan, Eun‐Jin Lee, Koichi Ito, Motoyuki Hattori

    Discovered via OpenAlex

  1226. Network Modeling Analysis in Health Informatics and Bioinformatics

    Structural exploration of Staphylococcus epidermidis virulence proteins for multi-epitope vaccine peptide design

    Nora Laref, Khadidja Belkheir

    Discovered via OpenAlex

  1227. Nature

    Computational design of metallohydrolases

    Donghyo Kim, Seth M. Woodbury, Woody Ahern, Doug Tischer, Alex Kang, Emily Joyce, Asim K. Bera, Nikita Hanikel, Saman Salike, Rohith Krishna, Jason Yim, Samuel J. Pellock, Anna Lauko, Indrek Kalvet, Donald Hilvert, David A. Baker

  1228. Nature Methods

    Atom-level enzyme active site scaffolding using RFdiffusion2

    Woody Ahern, Jason Yim, Doug Tischer, Saman Salike, Seth M. Woodbury, Donghyo Kim, Indrek Kalvet, Yakov Kipnis, Brian Coventry, Han Altae-Tran, Magnus S. Bauer, Regina Barzilay, Tommi Jaakkola, Rohith Krishna, David A. Baker

    Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.3 RoseTTAFold-based

  1229. Nature

    Computational enzyme design by catalytic motif scaffolding

    Markus Braun, Adrian Tripp, Morakot Chakatok, Sigrid Kaltenbrunner, C. Fischer, David B. Stoll, Aleksandar Bijelic, Wael Elaily, Massimo G. Totaro, Melanie Moser, Shlomo Yakir Hoch, Horst Lechner, Federico Rossi, Matteo Aleotti, Mélanie Hall, Gustav Oberdorfer

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.3 RoseTTAFold-based

  1230. PLoS Computational Biology

    BAGEL: Protein engineering via exploration of an energy landscape

    Jakub Lála, Ayham Al-Saffar, Stefano Angioletti‐Uberti

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 2. Model-based design · 2.4 LLM-based

  1231. Proceedings of the National Academy of Sciences

    Machine learning enables de novo multiepitope design of Plasmodium falciparum circumsporozoite protein to target trimeric L9 antibody

    Andrew Nelson, Samuel E. Garfinkle, Zi Jie Lin, Joyce H. Park, Amber Kim, Kelly Bayruns, Madison E. McCanna, Kylie M. Konrath, Colby J. Agostino, Daniel W. Kulp, Audrey R. Odom John, Jesper Pallesen

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.3 RoseTTAFold-based

  1232. Preprints.org

    A Systematic Survey on Generative Models for Graph Generation

    Jiarui Ji, Wenda Wang, Runlin Lei, Jialin Bi, Lei Wang, Rui Wang, Qiang Wang, Bin Tong, Xu Chen, Zhewei Wei

    Discovered via OpenAlex

  1233. Cells

    AI-Guided Dual Strategy for Peptide Inhibitor Design Targeting Structural Polymorphs of α-Synuclein Fibrils

    Jinfang Duan, Haoyu Zhang, Chuanqi Sun

    Discovered via OpenAlex

  1234. arXiv (Cornell University)

    Few-shot Protein Fitness Prediction via In-context Learning and Test-time Training

    Felix Teufel, Aaron W. Kollasch, Yining Huang, Ole Winther, Kevin Yang, Pascal Notin, Debora S. Marks

  1235. Communications Biology

    Decoding protein binding plasticity via integrated deep ribosome display and deep learning

    Mengtong Tang, Jiawei Li, Zhixi Li, Jingsong Cui, Hao Qi

    Discovered via OpenAlex

  1236. bioRxiv (Cold Spring Harbor Laboratory)

    Modeling the structure-conditioned sequence landscape for large-scale protein design with TriFlow

    Harish Srinivasan, Rongqing Yuan, Jing Zhang, Qian Cong, Jian Zhou

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 5.7 Flow-based · 5.Function to Sequence

  1237. Frontiers in Pharmacology

    Branched tetrameric lactoferricin peptides modified with diaminopropionic acid exhibit potent antimicrobial and wound-healing activities

    Nikitha Vavilthota, Gizem Babuççu, Robert A. Cordfunke, Leonie de Boer, Payal P. S. Balraadjsing, Bouke K. H. L. Boekema, Jan Wouter Drijfhout, Martijn Riool, Sebastian A. J. Zaat

    Discovered via OpenAlex

  1238. ChemRxiv

    Structure-based peptide design identifies inhibitors of the dyskerin/dyskerin interaction in H/ACA ribonucleoproteins targeting brain tumour cell lines

    Suzanne P. Van Wier, Zoë Rachael Goddard, Xiufen Lei, Ellen Hyde, Daniel J. Picard, Emily Hobson, Marco M. D. Cominetti, Maria Anne O'Connell, Mark Searcey, Marc Remke, Luiz O. F. Penalva, Andrew Michael Beekman

    Discovered via OpenAlex

  1239. MRS Bulletin

    Designing protein–material interfaces

    Shuai Zhang, Harley Pyles, David A. Baker, James J. De Yoreo

  1240. Journal of Neurochemistry

    Neuroprotective Effects of PEP ‐1‐ PGAM5 via the Attenuation of Oxidative Stress and Apoptosis in Parkinson's Disease

    Hyun Jung Kwon, Hyo Young Jung, Dae Young Yoo, Seung Myung Moon, Dae Won Kim

    Discovered via OpenAlex

  1241. Journal of Pharmacology and Experimental Therapeutics

    Pharmacological considerations for next-generation protein therapeutics in cardiovascular disease

    Emily Lin, Noor Momin

    Discovered via OpenAlex

  1242. Journal of Cheminformatics

    All-atom protein sequence design using discrete diffusion models

    Amelia Villegas-Morcillo, G. Admiraal, Marcel J. T. Reinders, Jana M. Weber

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 4.9 Diffusion-based · 4.Scaffold to Sequence

  1243. Food Bioscience

    Ancestral sequence reconstruction and rational protein design enhances lysozyme activity of helveticin NX371 against Bacillus cereus

    Qing Sun, Yong Hao, Yunbin Lyu, Zhaoxin Lu, Fanqiang Meng

    Discovered via OpenAlex

  1244. arXiv (Cornell University)

    Consistent Synthetic Sequences Unlock Structural Diversity in Fully Atomistic De Novo Protein Design

    Danny Reidenbach, Cao, Zhonglin, Zuobai Zhang, Kieran Didi, Tomas Geffner, Guoqing Zhou, Jian Tang, Christian Dallago, Arash Vahdat, Emine Küçükbenli, Karsten Kreis

    Discovered via OpenAlex

  1245. Small

    Integration of Generative Protein Design with Synthetic Porphyrin Assembly: Metal‐Responsive Cyclic Assembly of a Bi‐Porphyrin Acquisition Designer Protein (Small 49/2025)

    Hiroaki Inaba, Hiroki Onoda, Takayuki Uchihashi, Atsunori Oshima, Osami Shoji

    Discovered via OpenAlex

  1246. ImmunoTargets and Therapy

    Development of a Novel Anti-Siglec-15 Antibody for Tumor Immunotherapy

    Qin Liu, Lin Li, Siji Nian, Xiaoke Sun, Xiyuan Guo, Chengwen Li, Zhihui Yang, Yingchun Ye, Qing Yuan

    Discovered via OpenAlex

  1247. bioRxiv (Cold Spring Harbor Laboratory)

    Drug-like antibody design against challenging targets with atomic precision

    Chai Discovery Team, Jacques Boitreaud, Robert S. Chen, Jack Dent, Lucy Fairweather, Danny Geisz, Matthew Greenig, Nate Boyd, Jinay Jain, Brady Johnston, Matt McPartlon, Joshua Meier, Neil Patil, Zhuoran Qiao, Alex Rogozhnikov, Nathan Rollins, Nikitha Vicas, Paul Wollenhaupt, Kevin Wu, Andy Yeung

    Discovered via OpenAlex

  1248. Nature Methods

    Template-free antibody design

    Madhura Mukhopadhyay

    Discovered via OpenAlex

  1249. DOAJ (DOAJ: Directory of Open Access Journals)

    Development of a Novel Anti-Siglec-15 Antibody for Tumor Immunotherapy

    Liu Q, Li L, Nian S, Sun X, Guo X, Li C, Yang Z, Ye Y, Yuan Q

    Discovered via OpenAlex

  1250. IEEE Journal of Biomedical and Health Informatics

    MPSol: A Multimodal Prompt Learning Framework for Protein Solubility Prediction

    Yuhang Zhang, Peilin Chen, Keyan Ding, Han Liu, Shiqi Wang, Qi Song

    Discovered via OpenAlex

  1251. Genome biology

    A scalable equivariant graph network framework for precise protein function prediction

    Zixu Ran, Xudong Guo, Tong Pan, Yue Bi, Yi Hao, Heyun Sun, Jiangning Song, Fuyi Li

    Discovered via OpenAlex

  1252. arXiv (Cornell University)

    EnzyCLIP: A Cross-Attention Dual Encoder Framework with Contrastive Learning for Predicting Enzyme Kinetic Constants

    Khan, Anas Aziz, Fahad, Md Shah, Priyanka, Chandra, Ramesh, Singh, Guransh

    Discovered via OpenAlex

  1253. arXiv (Cornell University)

    RadDiff: Retrieval-Augmented Denoising Diffusion for Protein Inverse Folding

    Han, Jin, Tianfan Fu, Wu-Jun Li

    Discovered via OpenAlex

  1254. arXiv (Cornell University)

    Freeze, Diffuse, Decode: Task-Aware Adaptation of Transformer Embeddings for Antimicrobial Peptide Design

    Pankhil Gawade, Izdebski, Adam, Myriam Lizotte, Kevin R. Moon, Jake S. Rhodes, Guy Wolf, Ewa Szczurek

    Discovered via OpenAlex

  1255. Current Opinion in Biotechnology

    Advances and critical evaluation of autonomous protein engineering: towards transparent, accessible, and reproducible platforms

    Konstantin F. G. Weigmann, Uwe T. Bornscheuer, Mark Doerr

    Discovered via OpenAlex

  1256. arXiv (Cornell University)

    FoldSAE: Learning to Steer Protein Folding Through Sparse Representations

    Wojciech Zarzecki, Paulina Szymczak, Ewa Szczurek, Kamil Rafał Deja

    Discovered via OpenAlex

  1257. arXiv (Cornell University)

    Swarms of Large Language Model Agents for Protein Sequence Design with Experimental Validation

    Fiona Y. Wang, Di Sheng Lee, David Lee Kaplan, Markus J. Buehler

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 5.4 Transformer-based · 5.Function to Sequence

  1258. Nature Communications

    Ab-initio amino acid sequence design from protein text description with ProtDAT

    Xiao-Yu Guo, Yifan Li, Yuan Liu, Xiaoyong Pan, Hong‐Bin Shen

    Discovered via OpenAlex

  1259. Journal of Chemical Information and Modeling

    Rapid and Accurate Protein Structure Database Search Using Inverse Folding Model and Contrastive Learning

    Qiuyi Lyu, Hong Wei, Shuaishuai Chen, Zhenling Peng, Jianyi Yang

    Discovered via OpenAlex

  1260. Zenodo (CERN European Organization for Nuclear Research)

    A Critical Commentary on "Atomically accurate de novo design of antibodies with RFdiffusion" by Bennett et al., Nature 2025; doi: 10.1038/s41586-025-09721-5

    Zhu, Mengxi, Zhang, Yuxin, Zhu, Qinglan, Zhou, Shu-Feng

    Discovered via OpenAlex

  1261. Proceedings of the National Academy of Sciences

    Inhibition of ice recrystallization with designed twistless helical repeat proteins

    Robbert J. de Haas, Harley Pyles, Timothy F. Huddy, Jannick van Ossenbruggen, Chuanbao Zheng, Daniëlle van den Broek, Sanne N. Giezen, Ann Carr, Asim K. Bera, Alex Kang, Evans Brackenbrough, Emily Joyce, Banumathi Sankaran, David A. Baker, Ilja Karina Voets, Renko J. de Vries

    Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.3 RoseTTAFold-based

  1262. Journal of Agricultural and Food Chemistry

    Computationally Informed Redesign of Levansucrase from Erwinia tasmaniensis to Enhance Its Thermostability for Levan Biosynthesis

    Thanapon Charoenwongpaiboon, Yanisa Srichompoo, Karan Wangpaiboon, Stefano Benini, Robert A. Field, Chanchao Lorthongpanich, Piamsook Pongsawasdi, Rath Pichyangkura

    Discovered via OpenAlex

  1263. International Journal of Molecular Sciences

    Structure-Based Design and In Silico Evaluation of a Lipophilic Cyclooctanoyl- Derivative as a Renin Inhibitor: Lessons from Withdrawn Aliskiren

    Dimitrios Pavlos, Errikos Petsas, Filippos Panteleimon Chatzipieris, Thomas Mavromoustakos, Christos T. Chasapis

    Discovered via OpenAlex

  1264. Nature Communications

    Intravaginal delivery of mRNA-encoded antibodies with enhanced breadth and potency for SHIV/HIV protection

    Jae Yeon Joo, Peng Xiao, Susan P. John, Daryll A. Vanover, Hannah E. Peck, Loren E. Sasser, Deepanwita Bose, Younghun Jung, Jaehyeon Hwang, Chiara Zurla, Francois J. Villinger, Philip J. Santangelo

    Discovered via OpenAlex

  1265. Current Trends in Biotechnology and Pharmacy

    Sustainable Peptide synthesis and design: Integrating green synthesis and computational tools

    Priyanka Ray Choudhury, Sai Kumar Mishra, Shubhi Singh, Puniti Mathur

    Discovered via OpenAlex

  1266. Journal of the American Chemical Society

    De Novo Design of Peptide Masks Enables Rapid Generation of Conditionally-Active Miniprotein Binders

    Montserrat Escobar-Rosales, Cristina Montaner, Marc Expòsit, Roberta Lucchi, Cristina Díaz‐Perlas, David A. Baker, Benjamí Oller‐Salvia

  1267. bioRxiv (Cold Spring Harbor Laboratory)

    BoltzGen: Toward Universal Binder Design

    Hannes Stark, Felix Faltings, MinGyu Choi, Yuxin Xie, Eunsu Hur, Timothy J. O’Donnell, Anton Bushuiev, Talip Uçar, Saro Passaro, Weian Mao, Mateo Reveiz, Roman Bushuiev, Tally Portnoi, Tomáš Pluskal, Josef Šivic, Karsten Kreis, Arash Vahdat, Shamayeeta Ray, Jonathan T. Goldstein, Andrew Savinov, Jacob A. Hambalek, Anshika Gupta, Diego A. Taquiri-Diaz, Yaotian Zhang, Samuel J. Snyder, A. Katherine Hatstat, Angelika Arada, Nam Hyeong Kim, Haoyu Fan, Ethel Tackie‐Yarboi, Gene‐Wei Li, Lee Schnaider, Chang C. Liu, Gene‐Wei Li, Denes Hnisz, David M. Sabatini, William F. DeGrado, Jeremy Wohlwend, Gabriele Corso, Regina Barzilay, Tommi Jaakkola

  1268. arXiv (Cornell University)

    Beyond Protein Language Models: An Agentic LLM Framework for Mechanistic Enzyme Design

    Jacob, Bruno, Agarwal, Khushbu, Baer, Marcel, Rice, Peter, Raugei, Simone

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 5.4 Transformer-based · 5.Function to Sequence

  1269. bioRxiv (Cold Spring Harbor Laboratory)

    General-Purpose Large Language Models, such as DeepSeek V3.2, Have Evolved Protein Design Capabilities

    Jiawei Li, Xinxiu Dong

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 5.4 Transformer-based · 5.Function to Sequence

  1270. Biochemical Engineering Journal

    DLF-BBP: A novel deep learning framework for blood-brain barrier penetrating peptides design

    Lei Huang, Zhanglong Li, Hongjiang Li, Hongjiang Li, Tiejun Bing, Yingji Li, Changyuan Yu

    Discovered via OpenAlex

  1271. bioRxiv (Cold Spring Harbor Laboratory)

    CCK* (Convex Closure K*): A Suite of Algorithms for De Novo L- and D-peptide Design

    Henry Childs, Allen C. McBride, Bruce Randall Donald

    Discovered via OpenAlex

  1272. bioRxiv (Cold Spring Harbor Laboratory)

    Precision at Every Scale: Efficiency in AI-Driven De Novo Antibody Design

    Hyeonjin Cha, Kyesoo Cho, Jeonghyeon Gu, Daehyeon Gwak, Seung Woo Ham, Mirim Hong, Sehan Kim, Suyeon Kim, Sohee Kwon, Changsoo Lee, Dohoon Lee, Danyeong Lee, Dohoon Lee, Jungsub Lim, Jinsung Noh, Soyeon Oh, Taeyong Park, Seongchan Park, Taeyong Park, Eunwoo Ryu, Seongok Ryu, Deok Hyang Sa, Chaok Seok, Jiho Sim, Moo Young Song, Jonghun Won, Hyeonuk Woo, Jinsol Yang

    Discovered via OpenAlex

  1273. Nature Reviews Materials

    Engineering complexity into protein-based biomaterials for biomedical applications

    Nicole E. Gregorio, Cyrus M. Haas, Neil P. King, Cole A. DeForest

  1274. PLoS Computational Biology

    Automated and modular protein binder design with BinderFlow

    Nayim González-Rodríguez, Carlos Chacón-Sánchez, Óscar Llorca, Rafael Fernández-Leiro

    Discovered via OpenAlex

  1275. ACS Synthetic Biology

    Deep Learning-Based Prediction of Enzyme Optimal pH and Design of Point Mutations to Improve Acid Resistance

    Sizhe Qiu, Nan-Kai Wang, Yishun Lu, Jin‐Song Gong, Jin‐Song Shi, Aidong Yang

    Discovered via OpenAlex

  1276. ACS Catalysis

    ESTEEM Strategy: Revolutionizing Enzymatic Catalysis through the Evolutionary Gateway of Enzyme Tunnels

    Ruyue Dong, Jiaying Wang, Jian Tian, Guoshun Xu, Ziqi Liang, Xing Qin, Xiaolu Wang, Xiaoqing Liu, Huiying Luo, Bin Yao, Yaru Wang, Tao Tu

    Discovered via OpenAlex

  1277. European Journal of Medicinal Chemistry

    Synthetic α-glucosidase inhibitory peptides designed by molecular docking: In vitro screening and anti-hyperglycemic efficacy in diabetic mice

    Yanan Li, Wenxue Zhao, Liang Dong, Kai Xiang, Jun Ma, Hailin Cong, Bing Yu

    Discovered via OpenAlex

  1278. bioRxiv (Cold Spring Harbor Laboratory)

    Targeting peptide–MHC complexes with designed T cell receptors and antibodies

    Amir Motmaen, Kevin M. Jude, Nan Wang, Anastasia A. Minervina, David Feldman, Mauriz A. Lichtenstein, Abishai Ebenezer, Colin Correnti, Paul Glyndwr Thomas, K. Christopher García, David A. Baker, Philip H Bradley

    Curated by Papers for Protein Design Using Deep Learning · 4.5 GNN-based · 4.Scaffold to Sequence

  1279. Biomolecules

    Protein Engineering and Drug Discovery: Importance, Methodologies, Challenges, and Prospects

    Ahmed Mohammed, Nasir A. Ibrahim, Nosiba S. Basher

    Discovered via OpenAlex

  1280. Angewandte Chemie International Edition

    Water Networks as Hydrophobic Recognition Motifs in Proteins

    Serena G. Piticchio, Miriam Martínez‐Cartró, Salvatore Scaffidi, Sergio Rodríguez‐Arévalo, Andrea Bagán, Ainoa Sánchez‐Arfelis, S. Picaud, Tobias J. Krojer, P. Filippakopoulos, F. von Delft, Carmen Escolano, Carles Galdeano, Xavier Barril

    Discovered via OpenAlex

  1281. Zenodo (CERN European Organization for Nuclear Research)

    Conservative Motion Theory – Bio II Rational Enzyme Design via Conservative Flow Engineering

    Kawasaki, Hideyo

    Discovered via OpenAlex

  1282. Zenodo (CERN European Organization for Nuclear Research)

    Conservative Motion Theory – Bio IV Conservative Folding Flows and the Design of Functional Proteins

    Kawasaki, Hideyo

    Discovered via OpenAlex

  1283. ScholarsArchive (Brigham Young University)

    Navigating Structure, Function, and Stability: Bridging Immunotherapy and Protein Engineering in the Era of Machine Learning

    Haynie, Christopher J.

    Discovered via OpenAlex

  1284. Computers in Biology and Medicine

    Target-aware latent diffusion model for design of apoptosis-inducing anticancer peptides

    Tiara Natasha Binte Sayuti, Kakuly Mittal, Tan Lai Heng, Jagath Chandana Rajapakse

    Discovered via OpenAlex

  1285. Nature Communications

    Enhancing functional proteins through multimodal inverse folding with ABACUS-T

    Yufeng Liu, Rui Wu, Xinyu Wang, Sheng Wang, Ling-Hui Chen, Fudong Li, Quan Chen, Haiyan Liu

    Discovered via OpenAlex

  1286. Research Square

    The Biological Anchor: A Roadmap to Room-Temperature Quantum Communication by Co-opting Photosynthetic Coherence and De Novo Protein Design

    Alberto R. Mora Peña¹

    Discovered via OpenAlex

  1287. Angewandte Chemie International Edition

    Boosting Reversible Photocontrol of a Photoxenase by an Engineered Conformational Shift

    Sabrina Mandl, Janet H. Sanchez, Miquel Estévez‐Gay, Astrid Bruckmann, Caroline Hiefinger, Sílvia Osuna, Andrea Hupfeld

    Discovered via OpenAlex

  1288. Frontiers in Artificial Intelligence

    Designing novel peptides with amyloid-β binding and clearance potential using BiLSTM and molecular dynamics

    Vinod Kumar Yata, Om Pritam Das, Jarmani Dansana, Abhishikta Gadtya, Biswa Ranjan Meher, Sarad Pawar Naik Bukke, Narasaiah Kolliputi

    Discovered via OpenAlex

  1289. Journal of Agricultural and Food Chemistry

    Development of an Efficient Bifunctional Endoxylanase/Feruloyl Esterase Chimera for Coproduction of Ferulic Acid, p -Coumaric Acid, and Xylooligosaccharides

    Wenke Xiong, Yizhou Liu, Yingyu Shu, Shuangcheng Liang, Qiansi Chen, Xueao Zheng, Minghua Li, Ruoting Zhan, Kui Wang, Ying Zhang, Sidi Wang

    Discovered via OpenAlex

  1290. BMC Genomics

    MPIDNN-GPPI: multi-protein language model with an improved deep neural network for generalized protein‒protein interaction prediction

    Yane Li, Chengfeng Wang, Haibo Gu, Zhentao Long, Ming Fan, Lihua Li

    Discovered via OpenAlex

  1291. Zenodo (CERN European Organization for Nuclear Research)

    Co-folding of Carbohydrate-Protein Complexes

    Francesca Peccati

    Discovered via OpenAlex

  1292. eLife

    Kinesin-1 conformational dynamics are controlled by a cargo-sensitive TPR switch

    Shivam Shukla, Jessica A. Cross, Monika Kish, Sathish K.N. Yadav, Johannes F. Weijman, Laura O’Regan, Judith Mantell, Ufuk Borucu, Xiyue Leng, Christiane Schaffitzel, Jonathan J. Phillips, Derek N. Woolfson, Mark P. Dodding

    Discovered via OpenAlex

  1293. Nature Methods

    Multiplexed ultrasound imaging of gene expression

    Nivin N. Nyström, Zhiyang Jin, Marisa E. Bennett, Ruby Zhang, M Swift, Mikhail G. Shapiro

    Discovered via OpenAlex

  1294. arXiv (Cornell University)

    Full-Atom Peptide Design via Riemannian-Euclidean Bayesian Flow Networks

    Hao Qian, Shikui Tu, Lei Xu

    Discovered via OpenAlex

  1295. PubMed

    ApexGen: Simultaneous design of peptide binder sequence and structure for target proteins

    Xia, Xiaoqiong, César de la Fuente‐Núñez

    Discovered via OpenAlex

  1296. European Journal of Medicinal Chemistry

    Accelerated de novo design of xanthine oxidase-inhibitory peptides via physics-informed computational approaches

    Tianshuo Hu, Tianfei Yu, Kai Na, Qian Lin, Shujing Chen, Li Zhang, Chao Yu, Xiangyu Li, Xiaohua Guo

    Discovered via OpenAlex

  1297. Serican Journal of Medicine

    RFDiffusion: Revolutionizing Protein Design with Generative AI

    Zhangzhi Peng

    Discovered via OpenAlex

  1298. ACS Sensors

    Novel Near-Infrared Fluorescent Protein for Biliverdin Biosensing with a Hydrogel Scaffold

    Yufeng Zhao, Benjamin B. Kim, Victor Mun-Sing Sit, Lidija Malic, Teodor Veres, Michael Z. Lin

    Discovered via OpenAlex

  1299. Frontiers in Bioinformatics

    Machine learning-guided optimization of triple agonist peptide therapeutics for metabolic disease

    Anthony Wong, Sanskruthi Guduri, Tsung-Yen Chen, Kunal Patel

    Discovered via OpenAlex

  1300. bioRxiv (Cold Spring Harbor Laboratory)

    Sequence-aware Prediction of Point Mutation-induced Effects on Protein-Protein Binding Affinity using Deep Learning

    Jian Zhuang, Zonghui Li, Suhui Wang, Ren‐Chao Zheng, Guijun Zhang

    Discovered via OpenAlex

  1301. Cosmetics

    Development of New Anti-Wrinkle Peptide Using Cheminformatics-Assisted Peptidomimetic Design

    Soyoon Baek, Sekyoo Jeong, Seokjeong Yoon, Yeonjae Kim, Sungwoo Kim, Hwa-Jee Chung, Hyun‐Jung Kim, In Ki Hong, Gaewon Nam

    Discovered via OpenAlex

  1302. International Journal of Biological Macromolecules

    Advances in trypsin research: sources, structural insights, applications and protein engineering for industrial use

    Jia Chen, Guangyang Jiang, Yongqiang Tian

    Discovered via OpenAlex

  1303. Protein Science

    Multimodal diffusion for joint design of protein sequence and structure

    Shaowen Zhu, Siddhant Gulati, Yuxuan Liu, Siddhi Kotnis, Qing Hua Sun, Yang Shen

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.2 Diffusion-based

  1304. Biomacromolecules

    Building Thermosensitive Single-Component Protein Hydrogels from De Novo Designed Homodimers

    Jianglan Ning, Lurong Zhang, Yaxin Wang, Fenghui Guan, Sheng Ye

    Discovered via OpenAlex

  1305. Biomolecules

    Structural Basis for Targeting the Bifunctional Enzyme ArnA

    Xinyu Liu, Ruochen Yang, Libang Ren, Tong Li, Yanrong Li, Zhihua Yan, Yanrong Gao, Mingqi Yang, Jiazhi Li

    Discovered via OpenAlex

  1306. Journal of Medicinal Chemistry

    Selectivity Approaches in Therapeutic Antibody Design

    Mariam Ahmed Fouad

    Discovered via OpenAlex

  1307. PLoS Computational Biology

    OneProt: Towards multi-modal protein foundation models via latent space alignment of sequence, structure, binding sites and text encoders

    Klemens Flöge, Srisruthi Udayakumar, Johanna Sommer, Marie Piraud, Stefan Kesselheim, Vincent Fortuin, Stephan Günnemann, Karel J. van der Weg, Holger Gohlke, Erinç Merdivan, Alina Bazarova

    Discovered via OpenAlex

  1308. Optimizing Open Source Tools for Protein Design, Characterization, and Docking in Alzheimer's Disease Drug Development

    B.Vijaya Kumar

    Discovered via OpenAlex

  1309. arXiv (Cornell University)

    Controllable protein design with particle-based Feynman-Kac steering

    Erik Hartman, Jonas Wallin, Johan A. Malmström, Jimmy Olsson

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 2. Model-based design · 2.5 Sampling-algorithms · 3. Function to Scaffold · 3.4 Diffusion-based

  1310. Communications Chemistry

    Topological deep learning for enhancing peptide-protein complex prediction

    Xuhang Dai, Rui Wang, Yingkai Zhang

    Discovered via OpenAlex

  1311. IEEE Transactions on Artificial Intelligence

    A Comprehensive Review of Transformer-Based Language Models for Protein Sequence Analysis and Design

    Nimisha Ghosh, Daniele Santoni, Debaleena Nawn, Eleonora Ottaviani, Giovanni Felici

    Discovered via OpenAlex

  1312. bioRxiv (Cold Spring Harbor Laboratory)

    Global Analysis of Aggregation Determinants in Small Protein Domains

    Cydney M. Martell, Kamil K. Gebis, Han My Van, Yulia M. Gutierrez, Michelle D. Jung, Jeffrey N. Savas, Gabriel J. Rocklin

    Discovered via OpenAlex

  1313. Biomolecules

    De Novo Design of High-Affinity HER2-Targeting Protein Minibinders

    Yulin Zhao, Wenping Wei, Zijun Cheng, Min Yang, Yunjun Yan

    Discovered via OpenAlex

  1314. Advanced Functional Materials

    The Anisotropic Adsorption of De Novo Allosteric Two‐Component Protein Fibers on Mica Surfaces

    Chenyang Shi, Hao Shen, Yuna Bae, Jaeyoung Heo, Shuai Zhang, Lehan Yao, David A. Baker, James J. De Yoreo

  1315. bioRxiv (Cold Spring Harbor Laboratory)

    AstraBIND: Graph Attention Network for Predicting Ligand Binding Sites

    Aniruddh Goteti, Alexandra Vasilyeva, Çağlar Bozkurt

    Discovered via OpenAlex

  1316. The Open Biotechnology Journal

    De-Novo Protein Design Strategies for Targeting Rotavirus Proteins: Evolutionary Conservation and Therapeutic Implications

    Noura B. Abdulrahman, Noor M. Ahmed, Ahmed AbdulJabbar Suleiman

    Discovered via OpenAlex

  1317. ACS Omega

    Improving Stereochemical Limitations in Protein–Ligand Complex Structure Prediction

    Ryuichiro Ishitani, Yoshitaka Moriwaki

    Discovered via OpenAlex

  1318. bioRxiv (Cold Spring Harbor Laboratory)

    HalluDesign: Protein Optimization and de novo Design via Iterative Structure Hallucination and Sequence Design

    Minchao Fang, Chentong Wang, Jungang Shi, Fengbai Lian, Qihan Jin, Zhe Wang, Yanzhe Zhang, Peipei Chen, Zhanyuan Cui, Yanjun Wang, Ze Zhang, Yitao Ke, Qingzheng Han, Longxing Cao

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 2. Model-based design · 2.1.1 trRosetta-based

  1319. arXiv (Cornell University)

    Joint Design of Protein Surface and Structure Using a Diffusion Bridge Model

    Li, Guanlue, Xufeng Zhao, Fang Wu, Laue, Sören

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.2 Diffusion-based

  1320. bioRxiv (Cold Spring Harbor Laboratory)

    Pro4S: prediction of protein solubility by fusing sequence, structure, and surface

    Jie Qian, Lin Yang, Renxiao Wang, Yifei Qi

    Discovered via OpenAlex

  1321. Frontiers in Immunology

    Engineering HER2-targeted biparatopic antibodies to promote receptor internalization and restore antitumor efficacy

    Xinlin Liu, Wanpeng Yu, Yihuan Wang, Dongming Xing, Haiming Huang, Wenjing Zhu, Peng Sun

    Discovered via OpenAlex

  1322. ACS Omega

    PPAC: Predicting Protein–Protein Affinity Changes Induced by Amino Acid Mutations Using Protein Large Language Models

    Leilei Zhang, Xiaofei Zhou, Lu Liang, Jianping Lin

    Discovered via OpenAlex

  1323. Molecular Informatics

    RETRACTED: The Use of DeepQSAR Models for the Discovery of Peptides with Enhanced Antimicrobial and Antibiofilm Potential

    Jiaying You, Hazem Mslati, Evan F. Haney, Noushin Akhoundsadegh, Robert E. W. Hancock, Artem R Cherkasov

    Discovered via OpenAlex

  1324. Journal of Agricultural and Food Chemistry

    Engineering the Activity and Stability of dCMP Deaminase To Achieve Efficient and Simple Production of Uridine Monophosphate

    Zonglin Li, Ting Chen, Zhimin Li

    Discovered via OpenAlex

  1325. Nature

    Atomically accurate de novo design of antibodies with RFdiffusion

    Nathaniel R. Bennett, Joseph L. Watson, Robert J. Ragotte, Andrew J. Borst, DéJenaé L. See, Connor Weidle, Riti Biswas, Yutong Yu, Ellen L. Shrock, Russell Ault, Philip J. Y. Leung, Buwei Huang, Inna Goreshnik, John Tam, Kenneth D. Carr, Benedikt Singer, Cameron Criswell, Basile I. M. Wicky, Dionne K. Vafeados, Mariana Garcia Sanchez, Ho Min Kim, Susana Vázquez Torres, Sidney Chan, Shirley M. Sun, Timothy T. Spear, Yi Sun, Keelan O’Reilly, John M. Maris, Nikolaos G. Sgourakis, Roman A. Melnyk, Chang C. Liu, David A. Baker

    Curated by Papers for Protein Design Using Deep Learning · 5.12 Diffusion-based · 5.Function to Sequence

  1326. Structure

    Modular protein scaffold architecture and AI-guided sequence optimization facilitate de novo metalloenzyme engineering

    Paula Wagner Egea, Florent Delhommel, Ghulam Mustafa, Florian Leiss-Maier, Lisa Klimper, Thomas Badmann, Anna Heider, Idoia Wille, M. Groll, Michael Sattler, Cathleen Zeymer

    Discovered via OpenAlex

  1327. ChemRxiv

    PepComLibGen: A Web Server for Generating Peptide Libraries for Computer-Aided De Novo Peptide Design and Combinatorial Lead Optimization

    Sarfraz Ahmad, Muhammad Usman Mirza, John Frederick Trant

    Discovered via OpenAlex

  1328. arXiv (Cornell University)

    FP-AbDiff: Improving Score-based Antibody Design by Capturing Nonequilibrium Dynamics through the Underlying Fokker-Planck Equation

    Chen, Jiameng, Yida Xiong, Li, Kun, Zhang, Hongzhi, Xiantao Cai, Wenbin Hu, Jia Qing Wu

    Discovered via OpenAlex

  1329. Preprints.org

    Computational Design of a De Novo Binder for Claudin-6 (CLDN6)

    Jingxing Chen

    Discovered via OpenAlex

  1330. Proceedings of the National Academy of Sciences

    Modeling protein–small molecule conformational ensembles with PLACER

    Ivan V. Anishchenko, Yakov Kipnis, Indrek Kalvet, Guangfeng Zhou, Rohith Krishna, Samuel J. Pellock, Anna Lauko, Gyu Rie Lee, Linna An, Justas Dauparas, Frank DiMaio, David A. Baker

  1331. bioRxiv (Cold Spring Harbor Laboratory)

    Spontaneous Emergence of Symmetry in a Generative Model of Protein Structure

    Anton Oresten, Kenta Sato, Aron Stålmarck, Lukas Billera, Hedwig Nora Nordlinder, Jack Collier Ryder, Mateusz Kaduk, Ben Murrell

    Discovered via OpenAlex

  1332. AI-Guided Optimization of an Antimicrobial Peptide targeting Bacillus cereus: Enhancing Activity and Reducing Toxicity Through Machine Learning Tools

    Thakker, Shaurya

    Discovered via OpenAlex

  1333. Current Opinion in Biotechnology

    Artificial intelligence–powered biofoundries for protein engineering and metabolic engineering

    Junyu Chen, Nilmani Singh, Jingxia Lu, Stephan Lane, Huimin Zhao

    Discovered via OpenAlex

  1334. Nature Catalysis

    De novo design and evolution of an artificial metathase for cytoplasmic olefin metathesis

    Zhi Zou, Indrek Kalvet, Boris V. Lozhkin, Elinor Morris, Kailin Zhang, Dongping Chen, Marco L. Ernst, Xiang Zhang, David A. Baker, Thomas R. Ward

  1335. Proceedings of the National Academy of Sciences

    From sequence to scaffold: Computational design of protein nanoparticle vaccines from AlphaFold2-predicted building blocks

    Cyrus M. Haas, Naveen Jasti, Annie M. Dosey, Joel D. Allen, Rebecca A. Gillespie, Jackson McGowan, Elizabeth M. Leaf, Max Crispin, Cole A. DeForest, Masaru Kanekiyo, Neil P. King

    Curated by Papers for Protein Design Using Deep Learning · 4.5 GNN-based · 4.Scaffold to Sequence

  1336. JACS Au

    Designing Peptide Fossils That Model the Evolution of the Bacterial Ferredoxin Fold

    Bhanu P. Jagilinki, Ian J. Campbell, Alexei M. Tyryshkin, Andrew C. Mutter, Jan Siess, Juliana DiGiacomo, Dylan Klein, Saroj Poudel, Paul G. Falkowski, Jonathan J. Silberg, Vikas Nanda

    Discovered via OpenAlex

  1337. arXiv (Cornell University)

    DL4Proteins Jupyter Notebooks Teach how to use Artificial Intelligence for Biomolecular Structure Prediction and Design

    Chungyoun, Michael, Au, Gabe, Carpentier, Britnie, Puvada, Sreevarsha, Thomas, Courtney, Gray, Jeffrey J.

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 1. Reviews · 1.1 De novo protein design

  1338. Proceedings of the National Academy of Sciences

    Glycosylated cannabinoids meet computational enzyme design

    Joseph M. Jez

    Discovered via OpenAlex

  1339. Advanced Materials

    Engineered Protein‐Based Ionic Conductors for Sustainable Energy Storage Applications

    Juan David Cortés‐Ossa, Paolo Blesio, Marcial Fernández Castro, Lisa Almonte, Maxence Fernandez, Mantas Liutkus, Perumal Pandurangan, Carlos Sabater, Aitor Villaverde, Manuel Melle‐Franco, Nurit Ashkenasy, Felipe Jiménez‐Ángeles, Maria Carmen Morant‐Miñana, M. Reyes Calvo, Aitziber L. Cortajarena

    Discovered via OpenAlex

  1340. The Journal of Immunology

    An IL-21-derived neokine with enhanced anti-tumor efficacy 2594

    Suyasha Roy, Jung-Ho Chun, Birkley S. Lim, Michael J. Walsh, Kevin Zhangxu, Warren J. Leonard, Stephanie K. Dougan, Michael Lawrence Dougan, David A. Baker

  1341. The Journal of Immunology

    AI-based HIV-1 Env designs devoid of gp41 mimic native gp120 pre-fusion Env 9395

    Gyunghee Jo, Yoann Aldon, Naveen Jasti, Ja‐Hyun Koo, Joel D. Allen, Andy S. Tran, Rebecca Skotheim, David Juergens, Shivang Parikh, Joey H. Bouhuijs, Jonne L. Snitselaar, Wouter Olijhoek, Mark D. Langowski, Chelsea N. Fries, Tuğba Atabey, Mariëlle J. van Breemen, Marit J. van Gils, Max Crispin, Gabriel Ozorowski, Facundo D. Batista, Andrew B. Ward, David A. Baker, Rogier W. Sanders, Neil P. King

  1342. Briefings in Bioinformatics

    TCRdesign: an antigen-specific generative language model for de novo design of T-cell receptors

    Xiaokun Li, Qiang Yang, Long Xu, Weihe Dong, Kuanquan Wang, Suyu Dong, Wei Wang, Gongning Luo, Xianyu Zhang, Tiansong Yang, Xin Gao, Guohua Wang

    Discovered via OpenAlex

  1343. Briefings in Bioinformatics

    SAGE-prot: scoring-assisted generative exploration for multi-objective protein design

    Hocheol Lim, Geon-Ho Lee, Hyein Cho, Kyoung Tai No

    Discovered via OpenAlex

  1344. IEEE Transactions on Computational Biology and Bioinformatics

    De Novo Protein Structure Prediction by Model Quality Assessment Dynamic Feedback Mechanism Using Deep Learning

    Jun Liu, Guang-Xing He, Kailong Zhao, Xiaogen Zhou, Guijun Zhang

    Discovered via OpenAlex

  1345. Briefings in Bioinformatics

    MOFormer: navigating the antimicrobial peptide design space with Pareto-based multi-objective transformer

    Li Wang, Xiangzheng Fu, Jiahao Yang, Xinyi Zhang, Xiucai Ye, Tetsuya Sakurai, Xiangxiang Zeng, Yiping Liu

    Discovered via OpenAlex

  1346. Briefings in Bioinformatics

    Reinforcement learning with low-rank adaptation for targeted antimicrobial peptide design

    Juntae Park, Daehun Bae, Bongsung Bae, Hojung Nam

    Discovered via OpenAlex

  1347. The Journal of Immunology

    A Novel Biphasic Antibody Targeting TFRC and HER2 in Breast Cancer Treatment 9417

    Reagan Irene Farrell, Mei Li, Nicholas Pascuzzi, Kuan-Hui Chen, Xin Ge

    Discovered via OpenAlex

  1348. The Plant Journal

    PPEPFinder : A deep learning framework integrating sequence embeddings and structural graph representations for predicting fungal and oomycete effector proteins

    Mengdi Yuan, Shaoke Zhang, Jiajun Li, Jingyan Zheng, Chenping Lei, Zhuojun Wang, Miao Zhao, Wenyu Shi, Ziding Zhang

    Discovered via OpenAlex

  1349. BioDesign Research

    Advances in luminescence-based tracing technologies: applications and future perspectives

    Siyuan Sun, Tiange Wang, Yingzi Li, Hao Du

    Discovered via OpenAlex

  1350. Current Opinion in Biotechnology

    Large language model agents as experimental orchestrators in data-driven enzyme engineering

    Yuan Gao, Lihao Fu, Tong Si

    Discovered via OpenAlex

  1351. Scilight

    Refining Peptide Design for Surface Binding

    Alane Lim

    Discovered via OpenAlex

  1352. bioRxiv (Cold Spring Harbor Laboratory)

    A Genetic Algorithm to scour protein sequence space: A novel framework for protein engineering using protein language models and force fields

    João Sartori, Eduardo Krempser, Ana Carolina Ramos Guimarães, Lucas de Almeida Machado

    Discovered via OpenAlex

  1353. International Journal of Molecular Sciences

    Protein Design Meets Single-Molecule Detection: Towards Programmable Nanopore Sensors

    Xintong Liu, Chunfu Xu

    Discovered via OpenAlex

  1354. Journal of Chemical Information and Modeling

    Predicting Metalloprotein Redox Potentials with Machine Learning: A Focus on Iron–Sulfur Systems

    Francesca Persico, Bruno G. Galuzzi, Miriana Pellegrino, Anne-Lise Claudel, Luca DE GIOIA, Flavia Nastri, Gianfranco Gilardi, Chiara Damiani, Francesca Valetti, Marco Chino, Federica Arrigoni

    Discovered via OpenAlex

  1355. Journal of Peptide Science

    In Silico Peptide Design: Methods, Resources, and Role of AI

    Priyanka Ray Choudhury, Sai Kumar Mishra, Siddharth Yadav, Shubhi Singh, Puniti Mathur

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 1. Reviews · 1.2 Antibody design

  1356. Journal of Chemical Theory and Computation

    AbEgDiffuser: Antibody Sequence-Structure Codesign with Equivariant Graph Neural Networks and Diffusion Models

    Yibo Zhu, Xiumin Shi, Jingjuan Zhang, Weizhong Sun, Lu Wang

    Discovered via OpenAlex

    Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.2 Diffusion-based

  1357. bioRxiv (Cold Spring Harbor Laboratory)

    Ancient amino acid sets enable stable protein folds

    Valerio Guido Giacobelli, S. Andersson, Pavel Srb, Tereza Neuwirthová, Z. Ruszová, J. Marhoul, S. Pšenička, A. Knetl, Lucie Bednářová, Václav Veverka, Klára Hlouchová, Ingemar André

    Discovered via OpenAlex

  1358. bioRxiv (Cold Spring Harbor Laboratory)

    Improved De Novo Peptide Binder Design with Target-Conditioned Inverse Folding

    Elliot Layne, Ashlin K Kanawaty, Aron Broom, Alexander Kitaygorodsky, Anita K. Nivedha, Parth Vora, Caroline Woffindale, Sarah Hailstone, Eirini Sachouli, Ella Halcrow, Gillian E. Donachie, Michelle Adsett, Glenn L. Butterfoss, Mark Fingerhuth

    Discovered via OpenAlex