Machine Learning & Synthetic Biology

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October 23, 2026 Figshare
Echromatin: Developing a Cell-Free Gene Expression Platform Using Targeted Induced Steric Hinderance within DNA Arrays

Rory J Majule, Kyvalya Reddy, Oren Fox, Christopher N. Takahashi, Jeff Nivala
October 23, 2026 Figshare
Echromatin: Developing a Cell-Free Platform for Electronically Controllable Gene Expression

Rory J Majule, Kyvalya Reddy, Oren Fox, Christopher N. Takahashi, Jeff Nivala
October 21, 2026 Proceedings of the National Academy of Sciences
Molecular fossils of an ancestral code revealed by large-scale analysis of tRNAs

Ash Nova Royo, Paula Martín-Cabezas, Sergey Ovchinnikov, PAUL R. SCHIMMEL, Lluı́s Ribas de Pouplana
October 21, 2026 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
October 20, 2026 Zenodo (CERN European Organization for Nuclear Research)
Supplementary Data 2. Designed and predicted structures of all designs

Zachary Wu, Josh Abramson, Thomas Frerix, Alexander E. Chu, Ruijie Zhang, Luca Schulz, Amy E. Danson, Tristan O. C. Kwan, Li Kevin Wenliang, Zi‐Qi Li, Rosalia G. Schneider, Jacob Kelly, Ashok Thillaisundaram, Harshnira 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, John Jumper, Lucy J. Colwell, Demis Hassabis, Rob Fergus, Frances H. Arnold, Pushmeet Kohli, Jue Wang
October 19, 2026 arXiv (Cornell University)
Logit Averaging During Training Sets a New State of the Art for Non-Invasive Speech BCI

Miran Özdogan, Gereon Elvers, Michael M. Bronstein, Ōiwi Parker Jones
October 17, 2026 bioRxiv (Cold Spring Harbor Laboratory)
Multiplex programming of mappable, molecularly tagged genomic deletions

Aidan Keith, Riza M. Daza, Jonas Koeppel, Hanna Liao, David S. Lee, David K Moraes, Troy A. McDiarmid, Junhong Choi, Xiaoyi Li, Jean‐Benoît Lalanne, Chengxiang Qiu, Sudarshan Pinglay, Jay Shendure
October 17, 2026 arXiv (Cornell University)
Distribution-Based Regularization for Reward Fine-Tuning Diffusion and Flow Models

Romeo Passaro, Jeongjae Lee, Jong Chul Ye, Michael M. Bronstein, Yoshua Bengio, Alexander Tong, Danyal Rehman
October 17, 2026 npj Science of Food
De novo design of protein binders targeting the human sweet taste receptor as potential sweet proteins

Saisai Ding, Yi Zhang
Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.3 RoseTTAFold-based
October 16, 2026 arXiv (Cornell University)
World of SWECraft: Agent Collaboration at Scale via Simulated Software Worlds

Shannon Zejiang Shen, Yapei Chang, Qiyao Liang, Benjamin Newman, Jenny Liang, Rulin Shao, Ziqiao Ma, Junjie Oscar Yin, Yung-Sung Chuang, Weijia Shi, Yejin Choi, Luke Zettlemoyer, Pang Wei Koh, Mohit Iyyer, Tongshuang Wu, David Alexander Sontag
October 15, 2026 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
October 15, 2026 arXiv (Cornell University)
Interfaces and Modules: A Scalable Representation for Weight-Space Learning across Architectures

Michał Kozyra, Michael M. Bronstein
October 15, 2026 arXiv (Cornell University)
Normalizing Flow Maps

Francesco M. Ruscio, Timothy James Hitge, Fred Zhangzhi Peng, Danyal Rehman, Zander Blasingame, Nicholas M. Boffi, Michael M. Bronstein, Alexander Tong, Avishek Joey Bose
October 14, 2026 arXiv (Cornell University)
The COUNT: Counting N-grams Unlocks Scaling on Host Memory and Training-Free Adaptation

Ian Magnusson, Noah A. Smith, Pang Wei Koh
October 14, 2026 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
October 14, 2026 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
October 12, 2026 arXiv (Cornell University)
Intrinsic Geometry Matching: learning observation-equivariant process geometry

Manuel Lecha, Michael M. Bronstein, Iolo Jones
October 12, 2026 arXiv (Cornell University)
LLM-to-Flow Distillation: Teaching Natural Language Goals to Scientific Generators

Riccardo De Santi, Federico Di Gennaro, Angelo Gnazzo, Sophia Tang, Pranam Chatterjee, Fanny Yang, İsmail İlkan Ceylan, Michael M. Bronstein, Andreas Krause
October 9, 2026 bioRxiv (Cold Spring Harbor Laboratory)
High-throughput identification of chromatin-opening transcription factors

Aidan Keith, Shruti Jain, Riza M. Daza, Chengxiang Qiu, Pierre‐Luc Germain, Jay Shendure, Silvia Domcke
October 9, 2026 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
October 9, 2026 arXiv (Cornell University)
Multimodal Co-Generation With Continuous Bitstream Diffusion

Georgios Batzolis, Georgios Kontos, Bruno Trentini, Pranam Chatterjee, Micha Livne, Mark Girolami, Luca Ambrogioni
October 8, 2026 Science
A DNA Typewriter records the cell lineage history of a mouse, from zygote to late organogenesis

Qi Yu, Haedong Kim, Sophie Seidel, James F. Clark, Beth Martin, Kyle O'Connor, Riza M. Daza, Molly J. Gasperini, Jenny F. Nathans, Maggie Lam, Elena Gamo, Shruthi VijayKumar, Lauren M. Kuo, Jean‐Benoît Lalanne, Kamen P. Simeonov, Marion Pepper, Cole Trapnell, Jesse M. Gray, Junhong Choi, Chengxiang Qiu, Jay Shendure
October 8, 2026 arXiv (Cornell University)
Femtosecond Three-Dimensional Imaging of Single-Protein with Hard X-ray Laser

Paulrajpillai Lourdu Xavier, Andrew J. Morgan, Johan Bielecki, A. Samanta, Simon Dold, Chufeng Li, Xinyue Gao, Spencer K. Passmore, Ruslan P. Kurta, Tim B. Berberich, Emiliano De Santis, Wenhui Zhang, E Juncheng, F. Koua, Romain Letrun, Luca Gelisio, O. Turkot, E. V. Sobolev, Lukas V. Haas, Jannik Lübke, Jingxuan He, Madeline B. F. Memovich, Kevin Janson, Stefanie Lenzen, Safi Rafie-Zinedine, Mansi Butola, Oleksandr M. Yefanov, F. Trost, Chan Kim, Tomas Popelar, Tokushi Sato, Yevheniy Ovcharenko, Rebecca Boll, Sergey Usenko, Thomas M. Baumann, A. De Fanis, Björn Senfftleben, M. Porro, Andrea Castoldi, Ibrahym Dourki, Cyril Danilevski, Ekaterina S. Round, Christina Schmidt, Huijong Han, Roberto Alvarez, Ervin Chia, Cornelia Cazey, Carolin Seuring, Ruojie Sha, Maia Azubel, David A. Bushnell, Sébastien Boutet, Sergey Ovchinnikov, Adrian P. Mancuso⋈, Michael Meyer, Richard Bean, Anton Barty, Filipe R. N. C. Maia, Richard A. Kirian, Thomas D. Grant, N. Duane Loh, Carl Caleman, Erik G. Marklund, Nadia Zatsepin, Andrew V. Martin, S. Bajt, Roger D. Kornberg, Jochen Küpper, Henry N. Chapman
October 7, 2026 Science Advances
Machine learning–assisted directed evolution of plant Rubisco

Julie Lynn McDonald, Jiacheng Lin, Yunlong Zhao, Brian Hie, Rosemary J. Birch, Mary A. Gehring, Bryan D. Bryson, Spencer Michael Whitney, Matthew Donald Shoulders, Robert H. Wilson
October 6, 2026 Nature Biotechnology
Highly multiplexed mammalian metabolic engineering with a shotgun approach

Julie Trolle, Sara Sessa, Aleksandra M. Wudzinska, Mark Grivainis, Katerina Rincones, Tori C. Rodrick, Drew R. Jones, David Fenyö, Sudarshan Pinglay, Jef D. Boeke
October 6, 2026 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
October 6, 2026 Zenodo (CERN European Organization for Nuclear Research)
microsoft/dayhoff: v.0.1.3

Sarah Alamdari, Kevin Yang
October 6, 2026 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
October 6, 2026 arXiv (Cornell University)
Global Transport Couplings for Classifier-Free Guided Flows

Katarina Petrović, Zander Blasingame, Danyal Rehman, İsmail İlkan Ceylan, Michael M. Bronstein, Stephen Y. Zhang, Lazar Atanackovic, Alexander Tong
October 5, 2026 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
October 5, 2026 Nucleic Acids Research
OAS-nano: the Observed VHH Space Database

Clare M. C. Gillis, Klara Kropivšek, Ario de Marco, Olga Obrezanova, Erwin De Genst, Rebecca Croasdale-Wood, Charlotte Mary Deane, Matthew I. J. Raybould
October 2, 2026 bioRxiv (Cold Spring Harbor Laboratory)
A strategy for ionic current analysis of nanopore protein readouts

Andrew J. Stein, Neda Ghohabi Esfahani, Stuart Akeson, Pooria Daneshvar Kakhaki, Daphne Kontogiorgos-Heintz, Jeff Nivala, Miten Jain
October 2, 2026 arXiv (Cornell University)
Rubric-Based Optimization for Text-to-Music Generation

Ping Wang, Guang Yang, SU Shao-rong, Junkai Wu, Pang Wei Koh, Noah A. Smith
October 2, 2026 arXiv (Cornell University)
FrugalEvo: Towards Cost-Aware LLM-Guided Program Evolution

Hui Chen, Xuan Qi, James Zhao, Zhaopeng Feng, Shilong Liu, Kuang Xu, Pang Wei Koh, Bryan Hooi
October 1, 2026 Cell
A fluctuation test for gastruloid heterogeneity

Samuel G. Regalado, 承祥邱, Sanjay V. Kottapalli, Chau Huynh, Riza M. Daza, Aidan Keith, Jihye Park, Beth Martin, Wei Chen, Hanna Liao, Haedong Kim, Xiaoyi Li, Jean‐Benoît Lalanne, Nobuhiko Hamazaki, Silvia Domcke, Junhong Choi, Jay Shendure
October 1, 2026 Bioinformatics
SNOOPPI: a sequence-normalized database of on- and off-target protein–protein interactions

Sophia Vincoff, Pranam Chatterjee
October 1, 2026 bioRxiv (Cold Spring Harbor Laboratory)
pH-sensitive binder design with Proton-PottsMPNN

Christian P. Jacobsen, Lukas Deweid, Foster Birnbaum, Line W Gormsen, Thomas Fryer, Ulla Jagd, Andreas Hald, Morten Grønbech Rasch, Timothy P. Jenkins, Sergey Ovchinnikov
October 1, 2026 arXiv (Cornell University)
pCoMole: Pareto-Constrained Molecule Editing with Discrete Flows

Tong Chen, Maximilian Holsman, Lin Zhao, Pranam Chatterjee
October 1, 2026 arXiv (Cornell University)
Gacha Decoding: Eliciting Diverse Generations Through Instruction Following

Scott Geng, Yufei Zhang, Joseph Lee, Jerry Zheng Li, Marjan Ghazvininejad, Pang Wei Koh
October 1, 2026 arXiv (Cornell University)
ScholarCatalyst: A Benchmark for Retrieving Papers That Inspire New Research

Sohyeon Kim, Yoonho Lee, Bo Liu, Dayoon Ko, Rulin Shao, Seungone Kim, Graham Neubig, Pang Wei Koh, Aakanksha Chowdhery, Akari Asai, Omar Khattab, Yejin Choi, Gunhee Kim, Chelsea Finn
October 1, 2026 arXiv (Cornell University)
Higher-Order Molecular Grammars for Generative and Foundation Models in Chemistry

Yiming Huang, Yujie Zeng, Vijay Prakash Dwivedi, Simone Foti, Jianmin Wang, Jure Leskovec, Tolga Birdal
September 30, 2026 arXiv (Cornell University)
WorldAuditBench: Interactive 3D World Auditing with Multimodal Agents

Ziyan Jiang, Jingbo Yang, Jiabao Ji, Yujian Liu, Qiucheng Wu, Tommi Jaakkola, Yang Zhang, Shiyu Chang
September 30, 2026 arXiv (Cornell University)
UniEvo-VL: An On-policy Self-Distillation Training Recipe for Multimodal Model Self-improvement

Fang Wu, Da Xing, Yanjie Huang, Junxi Wang, Ji Wang, Hejia Geng, Guancheng Wan, Bowen Zuo, Xiaomin Li, Shixiang Tang, Xinyu Xiang, Zehong Wang, Shiyi Du, Peng Xia, Shuangjia Zheng, Yining Hong, Li Erran Li, Jure Leskovec, Yejin Choi
September 30, 2026 arXiv (Cornell University)
Specificity-Aware Diffusion Steering via Variance-Reduced Sequential Monte Carlo

Luran Wang, Linrui Ma, Hannes Stark, Regina Barzilay
September 29, 2026 arXiv (Cornell University)
Context Language Models

Rulin Shao, Shannon Zejiang Shen, Junjie Oscar Yin, Yuetai Li, 王敏衡, Hamish Ivison, Radha Poovendran, Nathan Lambert, Teng Xiao, Mike Lewis, Wen-tau Yih, Luke Zettlemoyer, Pang Wei Koh
September 28, 2026 bioRxiv (Cold Spring Harbor Laboratory)
Computational design of a versatile, zero-radius proximity labeling enzyme

Shizhong A. Dai, Peter E. Cavanagh, Albert Qiang, Zijuan Zhang, Qixiang Geng, Maribel Anguiano, Andrew G. Xue, Tsutomu Matsui, Khanh Nguyen, Namrata D. Udeshi, Sam Pellock, Brian Hie, Steven A. Carr, Christina K. Kim, Nathanael S. Gray, Wei Qin, Alice Y. Ting
September 28, 2026 bioRxiv (Cold Spring Harbor Laboratory)
Deep-learning-based design of an orthogonal self-labeling protein from K-Ras(G12C)

Jody Mou, Jing Wesley Leong, Sean Gao, Kaia Slaw, Michael McGill, Katherine A. Donovan, Rebecca J. Metivier, Franziska L. Sendker, Qi Kong, Diangen Lin, Azim M. Dharani, Xi Dawn Chen, Kevin M. Haigis, Eric S. Fischer, Fei Chen, Nicholas F. Polizzi
September 28, 2026 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
September 23, 2026 bioRxiv (Cold Spring Harbor Laboratory)
Coevolutionary mining of prokaryotic non-coding elements with a genome language model

David Li, Garyk Brixi, Alexandra Kim, Mateus Bernabe Fiamenghi, Claudia L. Driscoll, Simone A. Evans, Linyi Gao, Natalia Ivanova, Nikos C. Kyrpides, Karl A. Deisseroth, Max E. Wilkinson, Max E. Wilkinson, Brian Hie
September 21, 2026 Nature Structural & Molecular Biology
De novo design of semisynthetic conduction pores

Lee Schnaider, A. Katherine Hatstat, Alistair J. Scott, Sophia K. Tan, Richard G. Hambley, William Dawson, Rhys C. Griffiths, Rian C. Kormos, Arthur Alves de Melo, Eric Tse, Nicholas F. Polizzi, Elizabeth Jayne Wallace, Gregory E. Merz, William F. DeGrado
September 21, 2026 Zenodo (CERN European Organization for Nuclear Research)
PepRePs: Peptide-Retargeted Phosphatases via Generative Language Models

Lauren Hong, Tai-Chen Ho, Yi-Shiuan Tseng, Sophia Vincoff, Tong Chen, Connor Donahue, Matthew P. DeLisa, Po‐Han Chen, Pranam Chatterjee
September 18, 2026 bioRxiv (Cold Spring Harbor Laboratory)
Latent generative search unlocks de novo design of untapped biomolecular interactions at scale

Kieran Didi, Danny Reidenbach, Matthew Penner, Supriya Ravichandran, Marshall Case, Mike Nichols, Erik Swanson, Alex Reis, Maggie Prescott, Yue Hong Qian, Dongming Qian, J.S. Yang, Weiji Li, Le Li, Daichi Shonai, Sean M. Gay, Bhoomika Basu Mallik, Ho Yeung Chim, Liurong Chen, Miguel Atienza Juanatey, Hubert Klein, D. L. RIEGER, Phillip Schlegel, Anna U. Macintyre, Maxim Secor, Daniele Granata, Sooyoung Cha, Zhonglin Cao, Guoqing Zhou, Tomas Geffner, Xi Chen, Micha Livne, Zuobai Zhang, Tianjing Zhang, Kyle D. Gion, Michael M. Bronstein, Martin Steinegger, Kristine Deibler, Scott H. Soderling, Clara T. Schoeder, Alena Khmelinskaia, Florian Hollfelder, Christian Dallago, Emine Küçükbenli, Arash Vahdat, Pierce Ogden, Karsten Kreis
September 18, 2026 bioRxiv (Cold Spring Harbor Laboratory)
A Unified 3D Generative Model for Synthesizable Structure-Based Drug Design

Ilia Igashov, Arne Schneuing, Adrian W. Dobbelstein, Irina Morozova, Rebecca M. Neeser, Kara Zielinski, Luciano A. Abriata, Aaron S. Petruzzella, David Robin Pavel Iosub, Olivia Gampp, Artem Y. Lyubimov, Evgenia Elizarova, Isabella Ferrara, Pedro M. F. Sousa, Ana R. Lemos, Fabio Testori, Pierre A. Miranda Herrera, Laurin Kanis, Joseph Schmidt, Mac Kevin E. Braza, Rommie E. Amaro, Nicolas Thoma, Davide M. Ferraris, Roland Riek, James S. Fraser, Philippe Schwaller, Michael M. Bronstein, Bruno E. Correia
September 18, 2026 dCOBISS.SI Digital Repository
NatiNb: a naive llama VHH dataset

Klara Kropivšek, Henriette Capel, Clare M. C. Gillis, G. Gordon, Katharina Dost, Matthew I. J. Raybould, Charlotte Mary Deane, Ario de Marco
September 13, 2026 medRxiv
Resolving the Genomic Context of Clinically Relevant Antibiotic Resistance Genes in Wastewater with Ligation-Mediated PCR

Megan E. O’Brien, Bradie Ahern, Piper Brase, Sooyeol Kim, Caroline E. M. McCormack, Denise Garcia, Erika K. Keim, Erin Dahl, Matthew Feck, Kelly J. Kauber, Jorge A. Marchand, Rose S. Kantor, Amy J. Pickering, Breanna McArdle, Erica R. Fuhrmeister
September 12, 2026 bioRxiv (Cold Spring Harbor Laboratory)
Interaction Profiles as a Universal Language for Generative Molecular Design with ShEPhERD–2

Kento Abeywardane, Kenji Walker, Connor W. Coley
September 11, 2026 bioRxiv (Cold Spring Harbor Laboratory)
Reframing enzyme function prediction as conditional generation

William JF Rieger, Sebastian Haeussermann, Luca Herrmann, Zecheng Li, Béla P. Frohn, Manuel Maluenda, Gabriela Lobinska, Sahil Loomba, Julia C. Reisenbauer, Mikael Bodén A, Alexander Tong, Ariane Mora
September 10, 2026 bioRxiv (Cold Spring Harbor Laboratory)
AutoScreen: AI Co-Scientist System for Target Discovery in Functional Genomics

Yuanhao Qu, Xufeng Liu, Xiaotong Wang, Meitong Chen, Xiao Luo, Luna Lyu, Ming Yin, Jingwen Hui, Di Yin, Ravi K. Dinesh, Lin Qiu, Kexin Huang, Hanchen Wang, Shangyuan Tong, Henry C. Cousins, Ricky Feng, Oswaldo Martinez, Junze Zhang, Tanming Chen, Russ Biagio Altman, Jure Leskovec, Aviv Regev, Mengdi Wang, Le Cong
September 10, 2026 bioRxiv (Cold Spring Harbor Laboratory)
Generative Language Modeling for Antibody CDR Grafting and Alignment-driven De Novo Design

Ferran Gonzalez Hernandez, Oliver M. Turnbull, Maliha Sultana, Lorena Roldán-Martín, Rohan Kumar, Tom Diethe, Rebecca Croasdale-Wood, Charlotte Mary Deane, Dino Oglić
September 10, 2026 arXiv (Cornell University)
Data Scarcity and Model Sparsity: Mixtures-of-Experts Overfit More to Repeated Data

Atindra Jha, Margaret Li, Jure Leskovec, Percy Liang, Luke Zettlemoyer
September 9, 2026 bioRxiv (Cold Spring Harbor Laboratory)
COPAL: An ensemble of protein-ligand co-folding models enriches preferred ligand predictions for the LuxR-family of quorum sensing receptors

Davi Nakajima An, Amy L. Schaefer, Szu-Min Chang, Bianxia Bai, Charlotte Mulligan, Yasuhiro Oda, Everett Peter Greenberg, Frank DiMaio
September 9, 2026 Zenodo (CERN European Organization for Nuclear Research)
ShEPhERD-2 Supplementary Data

Kento Abeywardane, Kenji Walker, Connor W. Coley
September 8, 2026 Cell Reports Methods
Multimodal alignment improves generalizability of genomic biomarker prediction in computational pathology

Ekaterina Redekop, Eric Zimmermann, Ava P. Amini, Alex X Lu, Neil Tenenholtz, James Hall, Lorin A. Crawford, Kristen Severson
September 7, 2026 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
September 7, 2026 Machine Learning Health
Advancing knotted protein design with ESM3: guided generation and topological insights

Eva Marsalkova, Petr Šimeček
Curated by Papers for Protein Design Using Deep Learning · 5.4 Transformer-based · 5.Function to Sequence
September 5, 2026 bioRxiv (Cold Spring Harbor Laboratory)
Forecasting viral evolution from phylogenetic trees

Ivan Specht, Soyoon Park, Seyone Chithrananda, Claudia L. Driscoll, Garyk Brixi, Julia A. Palacios, Brian Hie
September 4, 2026 ChemRxiv
Modeling Reaction Feasibility to Identify New Opportunities for Sigmatropic Rearrangements

Jordan P. Liles, Nicholas Casetti, Thijs Stuyver, Connor W. Coley
September 4, 2026
Author response: Squidly harnesses enzyme functional hierarchy and contrastive learning to efficiently predict catalytic residues from sequence

William JF Rieger, Mikael Bodén A, Frances Arnold, Ariane Mora
September 4, 2026 Proceedings of the National Academy of Sciences
Systematic discovery of circular permutations across the protein universe using CIRPIN

Aiden R. Kolodziej, S. Mazdak Abulnaga, Sergey Ovchinnikov
September 3, 2026 bioRxiv (Cold Spring Harbor Laboratory)
Proteome-wide crosslinking mass spectrometry reveals novel components of essential complexes in Toxoplasma

Simon W Butterworth, Ashley L Gin, Shikha Shikha, Isadonna F. Tengganu, John Rush, Tom Duraisingh, Victoria Sodeinde, Leandro Lemgruber, Fabian Schulte, Ke Hu, Lilach Sheiner, Sergey Ovchinnikov, Sebastian Lourido
September 3, 2026 arXiv (Cornell University)
Efficient Test-Time Adaptation through Human-AI Interaction

Zora Zhiruo Wang, Apurva Gandhi, Rulin Shao, Aspen Chen, Jonas Weylin Mueller, Zhiqi Liang, Jett Chen, Michael Ryan, Qianou Ma, Luxi He, Zhoujun Cheng, Andre He, Seungone Kim, Jiayi Geng, Mingqian Zheng, Weiwei Sun, Zheyuan Zhang, Xinran Zhao, Yike Wang, Abe Hou, Liwei Jiang, Pang Wei Koh, Diyi Yang, Graham Neubig, Daniel Fried
September 2, 2026 Journal of the American Chemical Society
5- t Bu-Thalidomide Is a Selective Molecular Glue Degrader of the Transcription Factor FLT3 Interacting Zinc Finger 1 (FIZ1)

Patrick J. Brennan, Ruiyang Guo, Alban Ordureau, Sarah E. Singleton, Miranda Li, Fatma Albayrak Halaç, Connor H. Chang, Lorena Yu-Liao, Charlotte Mary Deane, Kendall N. Houk, Michael M. Hann, Lewis L. Brayshaw, Heeseon An, Stuart J. Conway
September 1, 2026 ChemRxiv
Fragment-Grounded Neural Simulation of Electron Ionization Mass Spectra at Library Scale

Magdalena Lederbauer, Runzhong Wang, Connor W. Coley
September 1, 2026 Cell Systems
Mapping the combinatorial coding between olfactory receptors and perception with deep learning

Seyone Chithrananda, Judith Amores, Kevin Yang
September 1, 2026 International Joint Conference on Artificial Intelligence
CollabLLM: From Passive Responders to Active Collaborators (Extended Abstract)

Shirley Wu, Michel Galley, Baolin Peng, Hao Cheng, G. L. Li, Yao Dou, Weixin Cai, James Zou, Jure Leskovec, Jianfeng Gao
September 1, 2026 arXiv (Cornell University)
Knowledge Distillation During Mid-Training Favors Reasoning over Factual Recall

Jacqueline He, Howard Yen, Shuyue Stella Li, Margaret Li, Hanqing Zeng, Yinglong Xia, Benyu Zhang, Zhuokai Zhao, Qiang Zhang, Pang Wei Koh, Luke Zettlemoyer, Wen-tau Yih
September 1, 2026 Immunological Reviews
Structural T‐Cell Receptor Analysis in the Age of Machine Learning

Nele P. Quast, Matthew I. J. Raybould, Charlotte Mary Deane
September 1, 2026 Zenodo (CERN European Organization for Nuclear Research)
Fragment-Grounded Neural Simulation of Electron Ionization Mass Spectra at Library Scale – Supplementary Data

Magdalena Lederbauer, Runzhong Wang, Connor W. Coley
August 31, 2026 Cell
Predicting cellular responses to perturbation across diverse contexts with State

Abhinav Adduri, Dhruv Gautam, Beatrice Bevilacqua, Mohsen Naghipourfar, Alishba Imran, Rohan Shah, Noam Teyssier, Rishi Verma, Christopher Carpenter, Basak Eraslan, Francis Chalissery, Rajesh Ilango, Vishvak Subramanyam, Chiara Ricci-Tam, Sanjay Nagaraj, Aidan F. Winters, Mingze Dong, Stefanie Fellinger, Adam Krejčí, Tilmann Bürckstümmer, Sravya Tirukkovular, Jeremy Sullivan, Brian S. Plosky, Nicholas D. Youngblut, Jure Leskovec, Luke A. Gilbert, Silvana Konermann, Patrick D. Hsu, Alexander Dobin, Dave P. Burke, Hani Goodarzi, Yusuf Roohani
August 28, 2026 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
August 28, 2026 Journal of the American Chemical Society
Ultrafast Proton-Coupled Electron Transfer Reactions at Unit Quantum Yield

Rui Liu, Zachary X. W. Widel, Jiaqi Zhu, Jarrett P. Mansergh, Aubrey R. Caplin, Samuel I. Mann, Ian J. Bakanas, Nicholas F. Polizzi, Peng Zhang, William F. DeGrado, David N. Beratan, Michael J. Therien
August 28, 2026 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
August 26, 2026 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
August 26, 2026 bioRxiv (Cold Spring Harbor Laboratory)
Hypothalamic Cell Type Evolution across Vertebrates

Yunming Wu, Prateek R Kalakuntla, Billie C. Goolsby, Yanay Rosen, Alyssa Hayashi, Guang Yang, Chew Chai, Heidi M. Tate, Tom Hindmarsh Sten, Jessica P. Nowicki, Lindsay L. Sailer, Jun Hyuk Song, Jaeyoon Lee, Robert C. Jones, Dong‐Wook Kim, David Kabelik, Alexander G. Ophir, Hongkui Zeng, Jure Leskovec, Stephen R. Quake, Lauren A. O’Connell, Bo Wang, Liqun Luo
August 26, 2026 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, Leyan Zhang, Yilin Fan, Peiyu Jiang, Yucen Huang, Geng Wu, Liyun Zhang, Liyun Zhang
Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.3 RoseTTAFold-based
August 24, 2026 Nature Biotechnology
Adaptive model-guided protein evolution with sparse data optimizes compact eukaryotic genome editors

Shijie Wan, Jackson Gold, Pranay Vure, Casey S. Mogilevsky, Ananya Talikoti, Tianrong Chen, Aman Gupta, Trisha Biswas, Zheng You, Vir Acharya, Pranam Chatterjee, Xiao Wang, Xue Gao
August 24, 2026 Nature Communications
Quantifying replication fidelity of unnatural base pairs using nanopore sequencing

Nicholas A. Kaplan, Jayson Sumabat, Jane McKelvey, Jeantine E. Lunshof, Jorge A. Marchand
August 24, 2026
Reviewer #2 (Public review): Protein generation with evolutionary diffusion: sequence is all you need

Sarah Alamdari, Nitya Thakkar, Rianne van den Berg, Neil Tenenholtz, Robert Strome, Alan M Moses, Alex X Lu, Nicolò Fusi, Ava P. Amini, Kevin K Yang
August 24, 2026
Reviewer #1 (Public review): Protein generation with evolutionary diffusion: sequence is all you need

Sarah Alamdari, Nitya Thakkar, Rianne van den Berg, Neil Tenenholtz, Robert Strome, Alan M Moses, Alex X Lu, Nicolò Fusi, Ava P. Amini, Kevin K Yang
August 20, 2026 Zenodo (CERN European Organization for Nuclear Research)
Supplementary Data for Modeling Reaction Feasibility to Identify New Opportunities for Sigmatropic Rearrangements

Nicholas Casetti, Jordan P. Liles, Thijs Stuyver, Connor W. Coley
August 19, 2026 Journal of the American Chemical Society
QuantumPioneer: Scalable Generation of Quantum Chemical Data for Solution-Phase Hydrogen Transfer Reactions

Haoyang Wu, Jonathan Wenyuan Zheng, Hao‐Wei Pang, Yu-Chi Kao, Akshat Shirish Zalte, Charlles R. A. Abreu, Emad Al Ibrahim, Sayandeep Biswas, Chansup Byun, Jackson W. Burns, Chuangchuang Cao, Yunsie Chung, Xiaorui Dong, Anna C. Doner, Jeremy Kepner, Bonhyeok Koo, Shih‐Cheng Li, Angiras Menon, Lauren Milechin, Nathan Morgan, Kariana Andrea Moreno-Sader, Kevin Spiekermann, Florence H. Vermeire, Bryan Wang, Markus Kraft, Connor W. Coley, William H. Green
August 18, 2026 bioRxiv (Cold Spring Harbor Laboratory)
Perturb-ME: Scalable mechanism discovery from phenotype-enriched genome-wide screens

Hanchen Wang, Jiacheng Gu, Chris J. Frangieh, Michael S. Cuoco, Maryann Zhao, Arindam Sett, Tom Beyer, Kuan Pang, Etzard Stolte, Zihan Xu, Jure Leskovec, Orit Rozenblatt–Rosen, Vivek Natarajan, Kathryn Geiger-Schuller, Pratiksha I. Thakore, Aviv Regev
August 17, 2026 Zenodo (CERN European Organization for Nuclear Research)
PolyDegLib

Joules Provenzano, Runzhong Wang, Connor W. Coley, Desirée L. Plata
August 17, 2026 arXiv (Cornell University)
Advancing Open and Reproducible Relational Learning: RelArena-$α$, TabPFN-Rel and RPI

Adrian Hayler, Klemens Flöge, Alan Arazi, Rishabh Ranjan, Jure Leskovec, Felix Birkel, Brendan Roof, Anurag Garg, Kristina Collins, Lydia Sidhoum, Jonas Kübler, Siyuan Guo, Oscar Key, Jan Hendrik Metzen, Rylee Grace, David Salinas, Arthur Cahu, Simon Bing, Benjamin Jäger, Tuana Celik, Mihir Manium, Vitor Monteiro, Jake Robertson, Jerry Chen, Eliott Kalfon, Tomás Pereda, Lilly Charlotte Wehrhahn, Dominik Safaric, Tobias Schroeder, Georg Grab, Diana Kriuchkova, Clara Cornu, Philipp Singer, Nick Erickson, Vahid Balazadeh, Marie Salmon, Simone Alessi, Kursat Kaya, Philipp Jund, Léo Grinsztajn, Yann LeCun, Bernhard Schölkopf, Madelon Hulsebos, Lennart Purucker, Sauraj Gambhir, Frank Hutter, Noah Hollmann
August 15, 2026 Zenodo (CERN European Organization for Nuclear Research)
Present and future of safe biological AI

Brian Hie
August 14, 2026 Nature Methods
Aligning protein-generative models to experimental fitness with ProteinDPO

Talal Widatalla, Ashir A. Borah, S. B. King, Claudia L. Driscoll, Rafael Rafailov, Brian Hie
Curated by Papers for Protein Design Using Deep Learning · 5.6 RL-based · 5.Function to Sequence
August 14, 2026 bioRxiv (Cold Spring Harbor Laboratory)
Protein language models and the long tail of functional diversity

Ria Vinod, Samir Char, Ava P. Amini, Lorin A. Crawford, Kevin Yang
August 12, 2026 Patterns
EmmaEmb: A quantitative framework for analyzing embedding spaces in molecular biology

Pia Francesca Rissom, Vít Škrhák, Paulo Yanez Sarmiento, Jordan F. Safer, Connor W. Coley, Bernhard Y. Renard, Henrike Heyne, Sumaiya Iqbal
August 11, 2026 bioRxiv (Cold Spring Harbor Laboratory)
Fast retrieval of structurally similar antibodies from large sequence databases with AbSLang

Eric Ji Da Wang, Fabian C. Spoendlin, Alexander Greenshields‐Watson, Christopher R. Taylor, Charlotte Mary Deane
August 10, 2026 Nature
Learning millisecond protein dynamics from what is missing in NMR spectra

Hannah K. Wayment-Steele, Gina El Nesr, Ramith Hettiarachchi, Adedolapo M. Ojoawo, Hasindu Kariyawasam, Sergey Ovchinnikov, Dorothee Kern
August 6, 2026 Science
Generative design of bacteriophages with genome language models

S. B. King, Claudia L. Driscoll, David B. Li, Daniel Guo, Aditi T. Merchant, Garyk Brixi, Max E. Wilkinson, Brian Hie
August 6, 2026 ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD)
CrediBench: Web-Scale Network Data for Credibility Prediction

Emma Kondrup, Sebastian Sabry, Hussein Abdallah, Zachary Yang, Jiaqi Xiong, Kellin Pelrine, James J. Zhou, Zhijin Guo, Michael M. Bronstein, Jean‐François Godbout, Reihaneh Rabbany K, Shenyang Huang
August 6, 2026 bioRxiv (Cold Spring Harbor Laboratory)
Characterizing the Assembly and Functional Properties of Gene-Length Mixed DNA Monolayers on Electrodes for Cell-Free Expression

Rory J Majule, Kyvalya Reddy, Samrutha Babu, Oren A. Fox, Jeff Nivala, Christopher N. Takahashi
August 4, 2026 bioRxiv (Cold Spring Harbor Laboratory)
De novo design of small-molecule–induced conformational change

Jeffrey Chang, Nicholas F. Polizzi
August 4, 2026 Preprints.org
Agentic Laboratories of the Future: Towards World Models for Scientific Discovery

Fu Kelsey, Luna Lyu, Shuzhen Li, Suozhi Huang, Suheng Xu, Joy Zheng, Xuefeng Liu, Shilong Liu, Greg Barbone, Ying Liu, Linxi Jim Fan, Yuke Zhu, Matthew Davis, Kaiyi Jiang, Sherry Yang, Xu Kuang, Yuan Luo, Francesca Dominici, Christina N. Curtis, Xiaojie Qiu, Alberto Abadie, Caroline Uhler, Mary X. Tang, Joseph C. Wu, Ju Li, Jared Toettcher, José L. Avalos‬, Rebecca B. Rojansky, Huimin Zhao, John P. A. Ioannidis, Barry Rand, Emma K. Lundberg, Andrew S. Rosen, Zhuang Liu, Shana Kelley, Chenyan Xiong, Barbara Elizabeth Engelhardt, Thomas Jude Montine, Christina V. Theodoris, Katherine Snowden Pollard, Fuxin Li, Xueyue Zhang, Tianyi Peng, Dmitri Basov, Xiang Qian, Eric Xing, Ali Yazdani, Jure Leskovec, Nigam Haresh Shah, Zhenan Bao, Pietro Perona, Sanfeng Wu, Clifford P. Brangwynne, Le Cong, Mengdi Wang
August 3, 2026 Zenodo (CERN European Organization for Nuclear Research)
AlphaFold3 predictions of 24 de novo designed lidded exatecan-binding proteins

Chang, Jeffrey, Nicholas F. Polizzi
July 31, 2026 bioRxiv (Cold Spring Harbor Laboratory)
Reconstructing whole-organism cell phylogenies with resolved ancestral transcriptional states

Zhan Liu, Shanjun Deng, Shanjun Deng, Mengdong Zhang, Boliang Liu, Huimin Xiang, Zhiyun Chen, Ao Zhang, Jay Shendure, Xionglei He
July 30, 2026 Zenodo (CERN European Organization for Nuclear Research)
De novo design of semisynthetic conduction pores - supplementary scripts

Lee Schnaider, William F. DeGrado, Samuel H. Schneider, Nicholas F. Polizzi
July 30, 2026 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
Curated by Papers for Protein Design Using Deep Learning · 4.1 MLP-based · 4.Scaffold to Sequence
July 30, 2026 bioRxiv (Cold Spring Harbor Laboratory)
The Human Bindome: A Proteome-scale Atlas of Designed Binder Candidates

Julius Wenckstern, Anna M. Díaz-Rovira, Julia Kuhn, Arvid Ban, Rahma Hamdani, Roser Pruano-Milla, Evgenia Elizarova, Sandrine Georgeon, Kaiden Thompson, Matthias Hinterndorfer, Devanarayanan Siva Sankar, Maximilian Dünnebacke, David Desscan, Sreenath Sasidharan Nair, Marcelo Querino Lima Afonso, Jennifer Fleming, Sameer S Velankar, Andrea Ablasser, Paola Picotti, Georg E. Winter, Mikko Taipale, Bruno E. Correia
Curated by Papers for Protein Design Using Deep Learning · 2. Model-based design · 2.1.1 trRosetta-based
July 29, 2026 PLoS Computational Biology
Integrating chemical structures as treatments improves representations of microscopy images for morphological profiling

Yemin Yu, Emre Hayir, Neil Tenenholtz, Lester W. Mackey, Ying Wei, David Alvarez-Melis, Ava P. Amini, Alex Xijie Lu
July 27, 2026 Proceedings of the National Academy of Sciences
Discovery of a phenazine–thiol conjugase from sparse data using genome-informed machine learning

Xiaoyu Shan, Inês B. Trindade, Nathaniel R. Glasser, Korbinian O. Thalhammer, Matthew Scurria, Ariane Mora, Stuart J. Conway, Dianne K. Newman
July 27, 2026 Zenodo (CERN European Organization for Nuclear Research)
Full raw sequencing dataset for "Quantifying replication fidelity of unnatural base pairs using nanopore sequencing"

Nicholas A. Kaplan, Jayson Sumabat, Jane McKelvey, Jeantine E. Lunshof, Jorge A. Marchand
July 25, 2026 bioRxiv (Cold Spring Harbor Laboratory)
Locus-Scale Massively Parallel Reporter Assays

Abby V. McGee, Carina G Biar, Beth Martin, Tony Li, Jean‐Benoît Lalanne, Haedong Kim, Jay Shendure
July 23, 2026 arXiv (Cornell University)
Expanding Flow Maps

Sophia Tang, Pranam Chatterjee
July 23, 2026 Science
Programmable design of synthetic plant immune receptors for pathogen protein recognition

Haocheng Zhu, Dandan Jiang, Qiao Zhang, Kang Zhang, Kevin Tianmeng Zhao, Jin‐Long Qiu, Caixia Gao
Curated by Papers for Protein Design Using Deep Learning · 2. Model-based design · 2.1.1 trRosetta-based
July 23, 2026 bioRxiv (Cold Spring Harbor Laboratory)
Programming protein shape as an explicit design layer via CAD blueprint-guided diffusion

Yilun Qi, Guoxun Zhang, Klaus Yserentant, Sonya Lee, Artem Y. Lyubimov, Kyrellos E. Ibrahim, Giuseppe Cimicata, James S. Fraser, Bo Huang, Tanja Kortemme
Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.3 RoseTTAFold-based
July 22, 2026 arXiv (Cornell University)
Antigen-specific Antibody Multi-modal Foundation Model for Functional Antibody Design

Xiaoliang Shi, Zichen Wang, Runze Ma, Zhongyue Zhang, Shuangjia Zheng
Curated by Papers for Protein Design Using Deep Learning · 5.4 Transformer-based · 5.Function to Sequence
July 21, 2026 Cell
Expanding the scope of protein language modeling to protein-protein interactions with MSA Pairformer

Yo Akiyama, Zhidian Zhang, Olivia Tang, Seongeun Kim, Milot Mirdita, Martin Steinegger, Sergey Ovchinnikov
July 21, 2026 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
Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.2 Diffusion-based
July 21, 2026 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
Curated by Papers for Protein Design Using Deep Learning · 3. Function to Scaffold · 3.4 Diffusion-based
July 17, 2026 bioRxiv (Cold Spring Harbor Laboratory)
Massively parallel characterization and predictive modelling of neuronal regulatory variation

Kilian Salomon, Chengyu Deng, Pyaree Mohan Dash, Theofilos Chalkiadakis, Qunrui Li, Ziwei Chen, Nicholas F. Page, Mustafa Helal, Sebastian Röner, Anshul Bharat Kundaje, Claudia Langenberg, Maik Pietzner, Jay Shendure, Max Schubach, Nadav Ahituv, Martin Kircher
July 16, 2026 Nature Communications
PeptiVerse: A unified platform for therapeutic peptide property prediction

Yinuo Zhang, Sophia Tang, Tong Chen, Elizabeth Mahood, Sophia Vincoff, Pranam Chatterjee
July 16, 2026 arXiv (Cornell University)
RetroAgent: Harnessing LLMs to Search Over Structured Memory for Agentic Retrosynthesis Planning

Yanqiao Zhu, Jingru Gan, Xiaoqi Sun, Fang Sun, Y Shi, Md Tauhidul Islam, Chao Shang, Wenhao Gao, Connor W. Coley, Yizhou Sun, Wei Wang
July 16, 2026 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
July 14, 2026 UNC Libraries
AI-driven discovery of synergistic drug combinations against pancreatic cancer

Regina Barzilay, Carleen A. Klumpp-Thomas, Tommi Jaakkola, Mohsen Pourmousa, Andrew Thieme, Zina Itkin, Sam Michael, Wengong Jin, Alexey V. Zakharov, Alexander Tropsha, Kelli Wilson, Travis Maxfield, Sankalp Jain, Cleber Camilo Melo-Filho, Marc Ferrer, Eugene N. Muratov, Joshua E. Hochuli, Noel Southall, Elena S. Barnaeva
July 14, 2026 bioRxiv (Cold Spring Harbor Laboratory)
De novo design of ligand binding and sensing with a physics based generative approach

Yanzhe Zhang, Yitao Ke, Rui Zhi, Qihan Jin, Yiqin Feng, Chentong Wang, Minchao Fang, Jinyang Liao, Dachuan Chen, Jiao Liu, Longxing Cao
Curated by Papers for Protein Design Using Deep Learning · 4.5 GNN-based · 4.Scaffold to Sequence
July 13, 2026 ChemRxiv
Chemical Shift Prediction Beyond the Electronic Structure Limit

Keir Adams, Corin Wagen, John Wolford, Marcus H. Sak, Josep Saurí, Zhitao Feng, Abhijeet S. Bhadauria, Michael A. Bailey, Jonah S. Downs, Sophia Z. Li, Amelia I. Liu, Tess Smidt, Robert S. Paton, Richard Y. Liu, Connor W. Coley, Eugene E. Kwan
July 13, 2026 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
July 10, 2026 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
Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.3 RoseTTAFold-based
July 10, 2026 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
Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.8 Flow-based
July 10, 2026 arXiv (Cornell University)
Vilya-1: An all-atom foundation model for macrocycle structure prediction and design

Vilya Research, Pascal Sturmfels, Milad Salem, Naozumi Hiranuma, Stephen Rettie, Xiaoliang Pan, Benjamin D. Sellers, Adam P. Moyer, Patrick J. Salveson, Ivan Anishchanka
Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.2 Diffusion-based
July 9, 2026 Science
Autonomous biomedical research with an artificial intelligence agent

Kexin Huang, Serena Zhang, Hanchen Wang, Yuanhao Qu, Yingzhou Lu, Ryan Li, Yusuf Roohani, Lin Qiu, Shiyi Cao, G. L. Li, Junze Zhang, Di Yin, Rick P. Wierenga, Deniz Kavi, Liu S, Tianwei She, Shruti Marwaha, Jennefer N. Carter, Xin Zhou, Matthew Thomas Wheeler, Jonathan Adam Bernstein, Mengdi Wang, Peng He, Jingtian Zhou, Michael P. Snyder, Le Cong, Aviv Regev, Jure Leskovec
July 9, 2026 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
July 9, 2026 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
July 9, 2026 bioRxiv (Cold Spring Harbor Laboratory)
IgGM2: An All-Atom Foundation Model for Adaptive Immune Receptor Design

J J Ma, Fandi Wu, Lin Yao, J Gao, Rubo Wang, Qifeng Li, Nianzu Yang, Songlin Jiang, Dawei Huang, Xiaoyong Pan, Yiheng Zhu, Tingjun Hou, Jianhua Yao, Junchi Yan
Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.9 AlphaFold-based
July 8, 2026 Nature
Universal cell embedding provides a foundation model for cell biology

Yanay Rosen, Yusuf Roohani, Ayush Agrawal, Leon Samotorcan, Stephen R. Quake, Jure Leskovec
July 8, 2026 Protein Science
Computational design of blue melanin by motif‐scaffolding a pentapeptide‐repeat protein

Di Sheng Lee, Bomi Park, Sergio Salgado, James Dolgin, David Lee Kaplan
Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.3 RoseTTAFold-based
July 7, 2026 Zenodo (CERN European Organization for Nuclear Research)
Predicted TCR:pMHC Structures

Benjamin McMaster, Ali El Moselhy, Ilija Ilievski, Christopher J. Thorpe, Nicole L. La Gruta, Jamie Rossjohn, Charlotte Mary Deane, Hashem Koohy
July 6, 2026 arXiv (Cornell University)
Rethinking Benchmarks and Models for Enzyme Specificity Prediction

Elizabeth H. Mahood, Natália Komorníková, Tomáš Pluskal, Pranam Chatterjee
July 3, 2026 bioRxiv (Cold Spring Harbor Laboratory)
A generalizable interface-seeded framework for de novo design of functional oligomers

Ho Yeung Chim, Mubarak Olanrewaju Idris, Dominic Rieger, Phillip Schlegel, Nicolas Manuel Goldbach, Miguel Atienza Juanatey, Bhoomika Basu Mallik, Stephen Buckley, Samrat Basak, Sandrine Georgeon, Kelvin Lau, Florence Pojer, Leonard Kaysser, Philip Tinnefeld, Clara T. Schoeder, Bruno E. Correia, Alena Khmelinskaia
Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.3 RoseTTAFold-based
July 2, 2026 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
July 2, 2026 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
June 30, 2026 arXiv (Cornell University)
SF-Cluster: Frustration-Guided MSA Subsampling for Alternative Protein Conformation Recovery

Hanqun Cao, Gao Z, Chunbin Gu, Ge Liu, Pheng Ann Heng, Pranam Chatterjee
June 29, 2026 bioRxiv (Cold Spring Harbor Laboratory)
OpenGerminal: an open-source implementation of the Germinal antibody design pipeline

Bing Han, Sheng Li
Curated by Papers for Protein Design Using Deep Learning · 4.5 GNN-based · 4.Scaffold to Sequence
June 28, 2026 arXiv (Cornell University)
GLACIER: Rethinking Mass Spectrum Prediction as an Object Detection Problem

Rui-Xi Wang, Runzhong Wang, Connor W. Coley
June 27, 2026 bioRxiv (Cold Spring Harbor Laboratory)
BoltzProt-1: Towards Efficient De Novo Binder Design with Good Developability

Talip Uçar, Jack Bates, Yunguan Fu, Wenxian Shi, Hannes Stark, Demitri Nava, Luca Cavalleri, Jeremy Wohlwend, Gabriele Corso, Saro Passaro
Curated by Papers for Protein Design Using Deep Learning · 2. Model-based design · 2.1.1 trRosetta-based
June 26, 2026 Zenodo (CERN European Organization for Nuclear Research)
ShuklaGroup/esmdynamic: esmdynamic

Diego E. Kleiman, Tom Sercu, Nikita Smetanin, Naail Kashif-Khan, Roshan Rao, Joshua Meier, jasoniliu, Chloe Hsu, Yinying Yao, Zeming Lin, Jacob Buswell Roberts, Alessandro Diana, Alex Morehead, Brian Hie, Walid Ahmad, Yunan Luo, brett koonce, cutecutecat, E Jinq Wong, Kira Mourão, S M Bonner
June 24, 2026 Nature
Zero-shot design of drug-binding proteins via neural iterative selection−expansion

Benjamin N. Fry, Kaia Slaw, Nicholas F. Polizzi
June 24, 2026 Journal of Chemical Information and Modeling
Pathway-Aware Template-Based Retrosynthesis

Jason J. Zhang, Seung Kyun Ha, Jihye Roh, Zhengkai Tu, Pritha Verma, Connor W. Coley, Klavs F. Jensen
June 24, 2026 bioRxiv (Cold Spring Harbor Laboratory)
Integrating Machine-learning and Ultra-high-throughput Screening for Enzyme spaces exploration

Yitao Ke, Yanzhe Zhang, Minchao Fang, Jingyang Zhao, Hao Zhu, Zehui Xu, Longxing Cao
Curated by Papers for Protein Design Using Deep Learning · 4.5 GNN-based · 4.Scaffold to Sequence
June 24, 2026 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
Curated by Papers for Protein Design Using Deep Learning · 2. Model-based design · 2.1.1 trRosetta-based
June 24, 2026 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
Curated by Papers for Protein Design Using Deep Learning · 4.5 GNN-based · 4.Scaffold to Sequence
June 23, 2026 Nature Biotechnology
Efficient generation of epitope-targeted antibodies with Germinal

Luis Santiago Mille, Claudia L. Driscoll, John N. Wang, Haoyu Dai, Talal Widatalla, Jim L. Zhang, Xiaowei Zhang, Bing Rao, Liang Feng, Brian Hie, Xiaojing J. Gao
June 23, 2026 bioRxiv (Cold Spring Harbor Laboratory)
A high-level programming language for generative biology with Proto

Aditi T. Merchant, Daniel Guo, Ben T Viggiano, Lucas Brennan-Almaraz, Evelyn Hur, Tina Mai, Peter Yin, Samuel H. King, Euan Angus Ashley, Brian Hie
June 22, 2026 arXiv (Cornell University)
Deciphering Fingerprints of 3D Molecular Surfaces for Accurate Epitope Prediction

Fang Wu, Weihao Xuan, Jure Leskovec, Yejin Choi, Li Erran Li
June 20, 2026 bioRxiv (Cold Spring Harbor Laboratory)
SAbDab2: The structural antibody database in the age of machine learning

Henriette Capel, Odysseas Vavourakis, Ben H. Williams, Christopher R. Taylor, Charlotte Mary Deane
June 20, 2026 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
Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.3 RoseTTAFold-based
June 19, 2026 bioRxiv (Cold Spring Harbor Laboratory)
Molecular basis of mitochondrial leucine transport by human Sideroflexin 1

Fiona Fitzpatrick, Daniel T.D. Jones, Hannah Aguirre, Benjamin N. Fry, Elena T. Kaemmerer, S. Tan, Luise E. Veelken, Wen Han Tong, Samuel Block, S. Ali Aghvami, Edmund R.S. Kunji, Nicholas F. Polizzi, Stephen C. Blacklow, Nora Kory
June 17, 2026 arXiv (Cornell University)
MassSpecGym in the Wild: Uncovering and Correcting Evaluation Pitfalls in AI-Driven Molecule Discovery

Hongxuan Liu, Roman Bushuiev, Ivy Lightheart, Mrunali Manjrekar, Anton Bushuiev, Magdalena Lederbauer, Filip Jozefov, Yinkai Wang, Soha Hassoun, Josef Šivic, James Taylor, Runzhong Wang, David Healey, Tomáš Pluskal, Connor W. Coley
June 17, 2026 Chemical Reviews
Membrane Protein Design: From Reprogramming Functions to AI-Guided De Novo Design Approaches

Jefferson Roberts, Patrick Barth
Curated by Papers for Protein Design Using Deep Learning · 1. Reviews · 1.1 De novo protein design
June 15, 2026 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
June 13, 2026 arXiv (Cornell University)
Spokes: Optimizing for Diverse Pretraining Data Selection

Clarence Lee, Yejin Choi, Luke Zettlemoyer, Pang Wei Koh, Hai Leong Chieu
June 12, 2026 Immunity
Analysis of monoclonal antibodies against the malaria invasion complex protein RIPR reveals the structural basis for synergistic antibody protection

Barnabas G. Williams, Jordan R. Barrett, Josefin Bartholdson Scott, Cassandra A. Rigby, Matteo Cagiada, Doris Quinkert, Kirsty McHugh, Anna Gesine Huhn, Sean A. Burnap, Camille Gourjault, Francesca Byrne, Sai Sundar Rajan Raghavan, Ana Rodrigues, Laura Bergamaschi, Beatrice Balzarotti, Simon J. Watson, Noah Miller, Lloyd D. W. King, Francesca R. Donnellan, Camilla A. Gladstone, Jemima Paterson, Stefania Scalabrino, Sarah E. Silk, Jo Salkeld, Angela M. Minassian, Katherine Skinner, Weston B. Struwe, Charlotte Mary Deane, Stephen T. Reece, Andrew B. Ward, Simon J. Draper
June 12, 2026 arXiv (Cornell University)
Riemannian Metric Matching for Scalable Geometric Modeling of Distributions

Jacob Bamberger, Adam Gosztolai, Pierre Vandergheynst, Michael M. Bronstein, Jones, Iolo
June 12, 2026 arXiv (Cornell University)
Emyx: Fast and efficient all-atom protein generation

Williams, Nicholas J., Ward Haddadin, Matteo Paolo Ferla, Constantin Schneider, Nicholas B. Woodall, Ruby Sedgwick, Christian Degnbol Madsen, Andrew L. Hopkins, Douglas E. V. Pires, Edward O. Pyzer‐Knapp
Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.8 Flow-based
June 11, 2026 Nature Metabolism
Why machine learning fails at mass spectrometry for small molecules

Ling Min Serena Khoo, Regina Barzilay
June 11, 2026 arXiv (Cornell University)
A2D2: Fine-Tuning Any-Length Discrete Diffusion for Adaptive Decoding

Sophia Tang, Y C Zhu, Molei Tao, Pranam Chatterjee
June 11, 2026 bioRxiv (Cold Spring Harbor Laboratory)
Deep learning based design of buried hydrogen bond networks with HBDesigner

Henry Dieckhaus, Brock T. Harvey, Tomiris Mulikova, Jessica T Horenstein, Nathan I. Nicely, Nicholas Z. Randolph, Brian A. Kuhlman
Curated by Papers for Protein Design Using Deep Learning · 4.5 GNN-based · 4.Scaffold to Sequence
June 11, 2026 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
June 10, 2026 Nature Communications
SciPhy: A Bayesian phylogenetic framework using sequential genetic lineage tracing data

Sophie Seidel, Antoine Zwaans, Samuel G. Regalado, Junhong Choi, Jay Shendure, Tanja Stadler
June 10, 2026 Stanford Digital Repository
Generative modeling with structured diffusion models

Minkai Xu, Stefano Ermon, Jure Leskovec, Lei Li, Stanford University. School of Engineering., Stanford University. Computer Science Department.
June 10, 2026 arXiv (Cornell University)
M*: A Modular, Extensible, Serving System for Multimodal Models

Atindra Jha, Naomi Sagan, Keisuke Kamahori, Irmak Sivgin, Rohan Sanda, Steven Gao, Mark Horowitz, Luke Zettlemoyer, Olivia Hsu, Jure Leskovec, Baris Kasikci, Stephanie Wang
June 10, 2026 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
Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.2 Diffusion-based
June 9, 2026 Nature Methods
Evaluating the role of pretraining dataset size and diversity on single-cell foundation model performance

Alan DenAdel, Madeline Hughes, Akshaya Thoutam, Anay Gupta, Andrew W. Navia, Nicolò Fusi, Srivatsan Raghavan, Peter S. Winter, Ava P. Amini, Lorin A. Crawford
June 9, 2026 Zenodo (CERN European Organization for Nuclear Research)
MSA Pairformer analysis data

Yo Akiyama, Zhidian Zhang, Olivia Tang, Seongeun Kim, Milot Mirdita, Martin Steinegger, Sergey Ovchinnikov
June 9, 2026 Nature
Author Correction: 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
June 8, 2026 arXiv (Cornell University)
Divide-and-Denoise: A Game-Theoretic Method for Fairly Composing Diffusion Models

A. Gupta, Polina Barabanshchikova, Vikas Garg, Samuel Kaski A, Tommi Jaakkola
June 8, 2026 bioRxiv (Cold Spring Harbor Laboratory)
ProtGPT3: an Open-source family of Promptable and Aligned Protein Language Models

Michele Garibbo, Gerard Boxo Corominas, Filippo Stocco, R. Illanes, Lasse Middendorf, Noelia Ferruz
Curated by Papers for Protein Design Using Deep Learning · 5.4 Transformer-based · 5.Function to Sequence
June 7, 2026 arXiv (Cornell University)
Few-step Cofolding with All-Atom Flow Maps

Gianluca Scarpellini, Ron Shprints, Peter Holderrieth, Juno Nam, Pranav Murugan, Rafael Gómez‐Bombarelli, Tommi Jaakkola, Maruan Al-Shedivat, Nicholas Matthew Boffi, Avishek Joey Bose
June 7, 2026 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
June 6, 2026 arXiv (Cornell University)
Diffusion Language Model Parallel Decoding via Product-of-Experts Bridge

Juntong Shi, Brian L. Trippe, Jure Leskovec, Stefano Ermon, Minkai Xu
June 4, 2026 bioRxiv (Cold Spring Harbor Laboratory)
Generative design of programmable asymmetric β-barrel nanopores

Annika Philomin, Ria Sonigra, Sagardip Majumder, Hsien-Jui Lin, Yanjing Li, Fanglei Xue, Ryan D. Kibler, Claire Baldus, Eva Trapido, Amelie Medeiros, Brian Coventry, Asim K. Bera, Alex Kang, Johnny Mendoza, Manish Kumar, Yi Yang, David A. Baker
Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.3 RoseTTAFold-based
June 3, 2026 Nature
Why a synthetic human genome is still worth building

Sudarshan Pinglay
June 3, 2026 arXiv (Cornell University)
AlloGen: Conformation-Selective Binder Generation with Differential State Scoring

Hanqun Cao, Zachary Quinn, Aastha Pal, Sumi Kimura, Jingjie Zhang, Pheng Ann Heng, Pranam Chatterjee
Curated by Papers for Protein Design Using Deep Learning · 3. Function to Scaffold · 3.4 Diffusion-based
June 3, 2026 Current Opinion in Chemical Engineering
Artificial Intelligence and Chemical Engineering: An Editorial Preface

Venkat Venkatasubramanian, Connor W. Coley
June 3, 2026 Nature Medicine
Reply to: Limited evidence of AI superiority in seasonal influenza vaccine strain selection

Wenxian Shi, Jeremy Wohlwend, Menghua Wu, Regina Barzilay
June 2, 2026 bioRxiv (Cold Spring Harbor Laboratory)
Gigabase-scale deletion scanning of the human genome

Jonas Koeppel, Aidan Keith, Samantha R. Sgrizzi, PeiXi Chen, Riza M. Daza, Faaiz Quaisar, Eleftheria Anastasia, Zihao Song, Jay Shendure, Sudarshan Pinglay
June 1, 2026 arXiv (Cornell University)
Why Are DMD Students Lazy? Understanding the Copying Behavior in Few-Step Distillation

Shucheng Li, Iolo Jones, Alexander Tong, Michael M. Bronstein
June 1, 2026 Worldwide Protein Data Bank
Structure of the PhiX174 bacteriophage

D.F. Li, S.H. King, C.L. Driscoll, Max E. Wilkinson, Brian Hie
June 1, 2026 Worldwide Protein Data Bank
Structure of the Evo-Phi36 bacteriophage

D.F. Li, S.H. King, C.L. Driscoll, Max E. Wilkinson, Brian Hie
June 1, 2026 arXiv (Cornell University)
AgentPLM: Agentic Protein Language Models with Reasoning-Augmented Decoding for Protein Sequence Design

Sahil Rahman, Maxx Richard Rahman
Curated by Papers for Protein Design Using Deep Learning · 5.4 Transformer-based · 5.Function to Sequence
May 30, 2026 Zenodo (CERN European Organization for Nuclear Research)
Systematic incorporation of non-natural base pairs for increased toehold-mediated strand displacement kinetics in random DNA pools — NAR 2026 submission

Tiernan Kennedy, T Mayer, Friedrich Simmel, Chris Thachuk
May 29, 2026 bioRxiv (Cold Spring Harbor Laboratory)
Just Add Structure: Protein Language Models Combined with Structural Equivariance Excel at Protein Tasks

Qurat-ul-ain, Carlos Outeiral, Matteo Cagiada, Yee Whye Teh, Charlotte Mary Deane
May 29, 2026 Figshare
FlowER - Mechanistic datasets and model checkpoint (May 29 2026)

Mun Hong Fong, Joonyoung F. Joung, Timothy M. Pinkhassik, Connor W. Coley
May 29, 2026 arXiv (Cornell University)
Graph Neural Networks Are Not Continuous Across Graph Resolutions

Christian Koke, Yuesong Shen, Abhishek Saroha, Marvin Eisenberger, Bastian Rieck, Michael M. Bronstein, Daniel Cremers
May 29, 2026 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
May 28, 2026 Journal of Clinical Oncology
Enabling federated discovery leveraging agentic AI systems: The Cancer AI Alliance and DataVoyager.

Simone E. Dekker, Stephen M. Salerno, Bodhisattwa Prasad Majumder, Reece Adamson, Rory Donovan-Maiye, Pang Wei Koh, Lei Deng, Keith D. Eaton, Srinivasan Yegnasubramanian, Kenneth L. Kehl, Justin Jee, Brian M. Bot, Jeff T. Leek, Cancer AI Alliance (CAIA)
May 26, 2026 arXiv (Cornell University)
Self-Improvement Imitation with Biologically Guided Search for Protein Design Under Oracle Budgets

Ashima Khanna, Dominik G. Grimm
Curated by Papers for Protein Design Using Deep Learning · 2. Model-based design · 2.5 Sampling-algorithms
May 25, 2026 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
Curated by Papers for Protein Design Using Deep Learning · 4.7 Transformer-based · 4.Scaffold to Sequence
May 25, 2026 arXiv (Cornell University)
JobBench: Aligning Agent Work With Human Will

Yuetai Li, Yichen Feng, Zhangchen Xu, Zixian Ma, Kaiyuan Zheng, Fengqing Jiang, Xinghua Sun, Rulin Shao, Zichen Chen, Yue Huang, Xinyang Han, Brian Lee, Kayla Xu, Shenglai Zeng, Hang Hua, Xiangliang Zhang, Basel Alomair, Ranjay Krishna, Luke Zettlemoyer, Pang Wei Koh, Bhaskar Ramasubramanian, Luyao Niu, Xiang Yue, Radha Poovendran
May 25, 2026 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
Curated by Papers for Protein Design Using Deep Learning · 2. Model-based design · 2.1.1 trRosetta-based
May 23, 2026 arXiv (Cornell University)
Found in Conversation: LLMs Teach Themselves to Close the Multi-Turn Gap

Tianlang Chen, Shirley Wu, Jure Leskovec
May 22, 2026 arXiv (Cornell University)
Diffusion Domain Expansion: Learning to Coordinate Pre-trained Diffusion Models

Egor Lifar, Semyon Savkin, Timur Garipov, Shangyuan Tong, Tommi Jaakkola
May 22, 2026 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
May 21, 2026 Communications Biology
ANARCII enables alignment-free antigen receptor numbering using a generalised language model

Alexander Greenshields‐Watson, Parth Agarwal, Sarah A. Robinson, Ben H. Williams, G. Gordon, Henriette Capel, Yushi Li, Fabian C. Spoendlin, Broncio Aguilar-Sanjuan, Fergus Boyles, Charlotte Mary Deane
May 21, 2026
DNAS-Bench: Deterministic Nucleic Acid Screener Benchmarking

Henry C. Wong, Tadayoshi Kohno, Jeff Nivala
May 20, 2026 bioRxiv (Cold Spring Harbor Laboratory)
Accurate protein stability prediction for small domains using mega-scale experiments

Yehlin Cho, Kotaro Tsuboyama, Theodore J. Litberg, Michelle Jung, Adunoluwa Obisesan, Wang, Qian, 1972-, Claire M. Phoumyvong, Jane Thibeault, Sergey Ovchinnikov, Gabriel J. Rocklin
May 20, 2026 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
May 19, 2026 Zenodo (CERN European Organization for Nuclear Research)
Raw BLI and SPR data

Xiaojing J. Gao, Claudia L. Driscoll, Luis Santiago Mille, Xiaojing J. Gao, Brian Hie, Haoyu Dai
May 19, 2026 arXiv (Cornell University)
MUX: Continuous Reasoning via Multiplexed Tokens

Ayhan Suleymanzade, Halil Alperen Gozeten, Michael M. Bronstein, İsmail İlkan Ceylan, Jinwoo Kim
May 18, 2026 arXiv (Cornell University)
Learning over Positive and Negative Edges with Contrastive Message Passing

Peter Pao-Huang, Charilaos I. Kanatsoulis, Michael D. Bereket, Jure Leskovec
May 18, 2026 arXiv (Cornell University)
Harnessing AtomisticSkills for Agentic Atomistic Research

Bowen Deng, Bohan Li, Matthew Cox, Hoje Chun, Juno Nam, Artur Lyssenko, Sathya Edamadaka, Jurğis Ruža, Xiaochen Du, Nofit Segal, Jesus Diaz Sanchez, Mingrou Xie, Ty Perez, Yu Yao, Miguel Steiner, Sauradeep Majumdar, Charles B. Musgrave, Anirban Chandra, Abhirup Patra, Detlef Hohl, Connor W. Coley, Ju Li, Rafael Gómez‐Bombarelli
May 15, 2026 bioRxiv (Cold Spring Harbor Laboratory)
Bio-BLIP: A Multimodal Architecture for Transferable Reasoning in Genomic Variant Interpretation

Anvita Gupta, Alejandro Buendia, Anshul Bharat Kundaje, Jure Leskovec
May 15, 2026 bioRxiv (Cold Spring Harbor Laboratory)
De novo design of transmembrane accessory subunits for fold stabilization and expansion

Sebastian Jojoa-Cruz, Saba Kanwal, Nolan P Jacob, Weiyi Tang, Mio Murakoso, Minghao Zhang, Jiayi Li, Masy Domecillo, Nicholas F. Polizzi, John R. Yates, Huong T. Kratochvil, Fábio Pereira Gomes, Heedeok Hong, Marco Mravic
May 15, 2026 Zenodo (CERN European Organization for Nuclear Research)
QuantumPioneer Dataset

Haoyang Wu, Jonathan Wenyuan Zheng, Hao‐Wei Pang, Yu-Chi Kao, Akshat Shirish Zalte, Charlles R. A. Abreu, Emad Al Ibrahim, Sayandeep Biswas, Chansup Byun, Jackson W. Burns, Chuangchuang Cao, Yunsie Chung, Xiaorui Dong, Anna C. Doner, Jeremy Kepner, Bonhyeok Koo, Shih‐Cheng Li, Angiras Menon, Lauren Milechin, Nathan Morgan, Kariana Andrea Moreno-Sader, Kevin Spiekermann, Florence H. Vermeire, Bryan Wang, Markus Kraft, Connor W. Coley, William H. Green
May 15, 2026 arXiv (Cornell University)
Entropy Across the Bridge: Conditional-Marginal Discretization for Flow and Schrödinger Samplers

Bruno Trentini, Dejan Dejan Stančević, Michael M. Bronstein, Alexander Tong, Luca Ambrogioni
May 14, 2026 bioRxiv (Cold Spring Harbor Laboratory)
BiomniBench: Process-level Evaluation of LLM Agents for Real-world Biomedical Research

Yuanhao Qu, Yingzhou Lu, Xinming Tu, Serena Zhang, Tianwei She, Alexander Glenn Shaw, Jou‐Ho Shih, Bingqing Zhao, Minjie Shen, Haochen Yang, Jielin Yan, Rongchuan Zhang, Xinze Wu, Tingting Li, Bin Zhou, Ning Wang, Adam Ma, Le Cong, Xiaobo Hu, Yuan Jiang, Jiayun Dong, Tao Peng, Jure Leskovec, Kexin Huang
May 13, 2026 bioRxiv (Cold Spring Harbor Laboratory)
Redesign selective protein binders using contrastive decoding

Ziwei Xie, Jinbo Xu
Curated by Papers for Protein Design Using Deep Learning · 4.7 Transformer-based · 4.Scaffold to Sequence
May 12, 2026 arXiv (Cornell University)
Deep Reasoning in General Purpose Agents via Structured Meta-Cognition

Dean Light, Michael Theologitis, Kshitish Ghate, Shuyue Stella Li, Benjamin Newman, Chirag Shah, Aylin Caliskan, Pang Wei Koh, Dan Mircea Suciu, Yulia Tsvetkov
May 10, 2026 arXiv (Cornell University)
TD3B: Transition-Directed Discrete Diffusion for Allosteric Binder Generation

Hanqun Cao, Aastha Pal, Sophia Tang, Yinuo Zhang, Jingjie Zhang, Pheng Ann Heng, Pranam Chatterjee
Curated by Papers for Protein Design Using Deep Learning · 4.9 Diffusion-based · 4.Scaffold to Sequence
May 9, 2026 BioData Mining
Generative models for antimicrobial peptide design: auto-encoders and beyond

Lukas Beierle, Julian M. Hahnfeld, Alexander Goesmann, Reihaneh Mostolizadeh, Franz Cemič
Curated by Papers for Protein Design Using Deep Learning · 1. Reviews · 1.3 Peptide design
May 8, 2026 ChemRxiv
QuADMET-Former: Pre-training on Quantum Mechanical Properties Improves ADMET Prediction

Arun Raja, Hongtao Zhao, Christian Tyrchan, Eva Nittinger, Michael M. Bronstein, Charlotte M. Deane, Garrett M. Morris
May 8, 2026 Zenodo (CERN European Organization for Nuclear Research)
SAbDab2 Machine Learning Dataset

Henriette Capel, Odysseas Vavourakis, Ben H. Williams, Christopher R. Taylor, Charlotte Mary Deane
May 7, 2026 bioRxiv (Cold Spring Harbor Laboratory)
Transforming the cytokine literature into a resource for experimental analysis and discovery

Lukas Oesinghaus, Molly Park, Rulin Shao, Pang Wei Koh, Georg Seelig
May 7, 2026 arXiv (Cornell University)
Training Transformers for KV Cache Compressibility

Yoav Gelberg, Yam Eitan, Michael M. Bronstein, Yarin Gal, Haggai Maron
May 6, 2026 medRxiv
SPARC: A mechanism-aware spatial representation from routine histology predicts cancer survival and therapy response

Aziz Ayed, Gabrielle Cohn, Noe Bertramo, Genevieve Marie Boland, Justin Gainor, Ömer H. Yilmaz, Regina Barzilay
May 6, 2026 bioRxiv (Cold Spring Harbor Laboratory)
Reverse engineering the fatally cross-reactive A3A TCR to decouple potency and specificity

Julia V McCarthy, A. Christina Heroven, King Ifashe, Martin Fellermeyer, Dan Hudson, Raul Cioaca, Max N Quastel, Yunkai Yang, Matteo Cagiada, Simeon D. Dragonov, Christopher J. Thorpe, Adán Pinto-Fernández, Alexander Greenshields‐Watson, Gillespie, Charlotte Mary Deane, Ricardo A. Fernandes
May 5, 2026 arXiv (Cornell University)
EvoLM: Self-Evolving Language Models through Co-Evolved Discriminative Rubrics

Shuyue Stella Li, Rui Xin, Teng Xiao, Yike Wang, Rulin Shao, Zoey Hao, Melanie Sclar, Sewoong Oh, Faeze Brahman, Pang Wei Koh, Yulia Tsvetkov
May 5, 2026 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
Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.2 Diffusion-based
May 5, 2026 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
Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.2 Diffusion-based
May 4, 2026 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
May 2, 2026 arXiv (Cornell University)
NoiseRater: Meta-Learned Noise Valuation for Diffusion Model Training

Haokai Zhao, Da Xing, Hanqun Cao, Tinson Xu, Xinyu Xiang, Yanchao Li, Xiangru Tang, Hongbin Lin, Zehong Wang, Kuan Pang, Peng Xia, Molei Tao, Li Erran Li, Aditya Joshi, Jure Leskovec, Fang Wu
May 1, 2026 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
Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.2 Diffusion-based
May 1, 2026 Journal of Biological Chemistry
Abstract 2231 Using neural networks to design proteins that bind and sense small-molecule drugs

Nicholas F. Polizzi
May 1, 2026 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
Curated by Papers for Protein Design Using Deep Learning · 4.3 LSTM-based · 4.Scaffold to Sequence
April 30, 2026 Science
Toward life with a 19–amino acid alphabet through generative artificial intelligence design

Liyuan Liu, Charlotte Rochereau, Simon Kozlov, Guillaume Urtecho, Xiaonan Liu, Jiahui Zhao, Jasmine Wang, Yiming Huang, Yiming Qu, Zetian Zhang, Tomasz Blazejewski, Avi Swartz, Sergey Ovchinnikov, Harris H. Wang
April 30, 2026 medRxiv
A biologically annotated neural network for proteomic discovery in Parkinson’s disease

Avish Vijayaraghavan, Lorin A. Crawford, Saboo Krishnakant, Ava P. Amini, Ashley Mae Conard, Abby L. Olsen, Lana M. Chahine, Kristen Severson
April 30, 2026 bioRxiv (Cold Spring Harbor Laboratory)
TxConformal: Controlling False Discoveries in AI-Driven Therapeutic Discovery

Ying Jin, Kexin Huang, Nathaniel Diamant, Kerry R. Buchholz, Steven T. Rutherford, Nicholas Skelton, Tommaso Biancalani, Gabriele Scalia, Jure Leskovec, Emmanuel J. Candès
April 30, 2026
Author response for "A Machine Learning-Based Workflow for Transaminase Selection"

Alexander J. Rago, Priyanka Raghavan, Lisandra Santiago-Capeles, Ruijie Zhang, ying wang, Connor W. Coley
April 30, 2026 arXiv (Cornell University)
Towards A Generative Protein Evolution Machine with DPLM-Evo

Xinyou Wang, Liang Hong, Jiasheng Ye, Zaixiang Zheng, Yu Li, Shujian Huang, Quanquan Gu
Curated by Papers for Protein Design Using Deep Learning · 5.12 Diffusion-based · 5.Function to Sequence
April 29, 2026 Proceedings of the National Academy of Sciences
Computational design of an ultrapotent deltacoronavirus miniprotein inhibitor

Nathan G Avery, Courtney N. Yoshiyama, Ashley L Taylor, Young‐Jun Park, Daniel E. Asarnow, Lisa Perruzza, Jack T Brown, Davide Corti, Fabio Benigni, Tyler N. Starr, David Veesler
Curated by Papers for Protein Design Using Deep Learning · 2. Model-based design · 2.1.1 trRosetta-based
April 28, 2026 Nature Communications
Technical and biological sources of noise confound multiplexed enhancer AAV screening

Avery C. Hunker, John K. Mich, Naz Taskin, Amy Torkelson, Trangthanh Cardenas, Jean‐Benoît Lalanne, Joseph T. Mahoney, Darren Bertagnolli, Anish Bhaswanth Chakka, Rushil Chakrabarty, Nicholas P. Donadio, Rebecca Ferrer, Molly J. Gasperini, Jeff Goldy, Junitta Guzman, Kelly Jin, Shannon Khem, Rana Kutsal, Refugio A. Martinez, Dakota Newman, Nick Pena, Christine Rimorin, Dana Rocha, Nadiya V. Shapovalova, Michael Tieu, Natalie Weed, Thomas Zhou, Rebecca Hodge, Shenqin Yao, Jay Shendure, Kimberly A. Smith, Ed S. Lein, Bosiljka Tasic, Boaz P. Levi, Jonathan T. Ting
April 28, 2026 Nature Biotechnology
Pool-packaged AAV libraries exhibit extensive length-dependent and homology-dependent chimerism

Jean‐Benoît Lalanne, Chau Huynh, John K. Mich, Avery C. Hunker, Troy A. McDiarmid, Haedong Kim, Boaz P. Levi, Jonathan T. Ting, Jay Shendure
April 28, 2026 eLife
Optics-free reconstruction of shapes, images and volumes with DNA barcode proximity graphs

Hanna Liao, Sanjay V. Kottapalli, Yuqi Huang, Matthew Chaw, Jase Gehring, Olivia Waltner, Melissa Phung-Rojas, Riza M. Daza, Frederick A. Matsen IV, Cole Trapnell, Jay Shendure, Sanjay R Srivatsan
April 28, 2026
Reviewer #1 (Public review): Optics-free reconstruction of shapes, images and volumes with DNA barcode proximity graphs

Hanna Liao, Sanjay V. Kottapalli, Yuqi Huang, Matthew Chaw, Jase Gehring, Olivia Waltner, Melissa Phung-Rojas, Riza M. Daza, Frederick A. Matsen IV, Cole Trapnell, Jay Shendure, Sanjay R Srivatsan
April 28, 2026
Author response: Optics-free reconstruction of shapes, images and volumes with DNA barcode proximity graphs

Hanna Liao, Sanjay V. Kottapalli, Yuqi Huang, Matthew Chaw, Jase Gehring, Olivia Waltner, Melissa Phung-Rojas, Riza M. Daza, Frederick A. Matsen IV, Cole Trapnell, Jay Shendure, Sanjay R Srivatsan
April 28, 2026 Science China Life Sciences
TcrDesign: de novo design of epitope-specific full-length T cell receptors

Kaixuan Diao, Jing Chen, Xiangyu Zhao, Tao Wu, Die Qiu, W Wang, Haopeng Wang, Xue-Song Liu
Curated by Papers for Protein Design Using Deep Learning · 5.4 Transformer-based · 5.Function to Sequence
April 27, 2026 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, David A. Baker
April 27, 2026 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
April 25, 2026 bioRxiv (Cold Spring Harbor Laboratory)
Are Current AI Virtual Cell Models Useful for Scientific Discovery?

Michael D. Bereket, Jure Leskovec
April 24, 2026 Nature Cell Biology
The proteomic landscape and temporal dynamics of human and mouse gastruloid development

Riddhiman K. Garge, Valerie Lynch, Rose Fields, Silvia Casadei, Sabrina Best, Jeremy Stone, Matthew W. Snyder, Connor A. Kubo, Arata Wakimoto, Zukai Liu, Christopher D. McGann, Jay Shendure, Lea M. Starita, Nobuhiko Hamazaki, Devin K. Schweppe
April 22, 2026 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
April 22, 2026 bioRxiv (Cold Spring Harbor Laboratory)
De novo masking domains that gate TNF-family ligand assembly and activity

Shota Kudo, Brian A. Kuhlman
Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.3 RoseTTAFold-based
April 21, 2026 Environmental Science & Technology
Hydrolysis Reaction Rate Prediction Using Machine Learning: WaterDRoP

Amélie C. Lemay, Connor W. Coley, Desirée L. Plata
April 21, 2026 bioRxiv (Cold Spring Harbor Laboratory)
Multi-scale dissection, compaction and derivatization of mammalian developmental enhancers

Jean‐Benoît Lalanne, Tony Li, Emma A.N. Kajiwara, Chau Huynh, Tiffany V. Do, Beth K. Martin, Samuel G. Regalado, Jay Shendure
April 21, 2026 bioRxiv (Cold Spring Harbor Laboratory)
Retracing and rewriting the evolutionary trajectories of mammalian developmental enhancers

Tony Li, Jean‐Benoît Lalanne, Emma A.N. Kajiwara, Shruti Jain, Xiaoyi Li, Tiffany V. Do, Beth K. Martin, Samuel G. Regalado, Riza M. Daza, Jay Shendure
April 20, 2026 ACM SIGKDD Conference on Knowledge Discovery and Data Mining (KDD)
AbFlow: End-to-end Paratope-Centric Antibody Design by Interaction Enhanced Flow Matching

Wenda Wang, Yang Zhang, Zhewei Wei, Wenbing Huang
Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.8 Flow-based
April 19, 2026 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
April 19, 2026 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
April 18, 2026 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
Curated by Papers for Protein Design Using Deep Learning · 4.9 Diffusion-based · 4.Scaffold to Sequence
April 17, 2026 arXiv (Cornell University)
FRIGID: Scaling Diffusion-Based Molecular Generation from Mass Spectra at Training and Inference Time

Montgomery Bohde, Hongxuan Liu, Mrunali Manjrekar, Magdalena Lederbauer, Shuiwang Ji, Runzhong Wang, Connor W. Coley
April 16, 2026 bioRxiv (Cold Spring Harbor Laboratory)
Sampling antibody conformational ensembles with ABodyBuilder4-STEROIDS

Fabian C. Spoendlin, Matteo Cagiada, King Ifashe, Odysseas Vavourakis, Charlotte Mary Deane
April 16, 2026 Zenodo (CERN European Organization for Nuclear Research)
mRNAutilus Training Data (Pretraining + Classifiers)

Smit Patel, Pranam Chatterjee, Sherwood Yao, Sophia Tang
April 16, 2026 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
Curated by Papers for Protein Design Using Deep Learning · 5.4 Transformer-based · 5.Function to Sequence
April 15, 2026 bioRxiv (Cold Spring Harbor Laboratory)
Evolutionary conditioning enables guided generation of functionally diverse enhancers

Andrew Duncan, Micaela Elisa Consens, Lorin A. Crawford, Jennifer A. Mitchell, Alan M Moses, Kevin Yang, Alex X Lu
April 15, 2026 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
Curated by Papers for Protein Design Using Deep Learning · 4.5 GNN-based · 4.Scaffold to Sequence
April 14, 2026 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
April 14, 2026 arXiv (Cornell University)
KumoRFM-2: Scaling Foundation Models for Relational Learning

Valter Hudovernik, Federico Elizondo Lopez, Vid Kocijan, Akihiro Nitta, Jan Eric Lenssen, Jure Leskovec, Matthias Fey
April 13, 2026 Nature Chemistry
tRNA-deacylase-directed discovery of biosynthetic pathways

Douglas C. Millar, Yu Zhou, Jorge A. Marchand, Helena Roberts-Mataric, Tavis Chen, Calvin X. Hu, Jason Fang, Shannon Millar, Elizabeth A. Stone, Jeffrey G. Pelton, Max B. Sosa, Michelle C. Y. Chang
April 13, 2026 arXiv (Cornell University)
A Mechanistic Analysis of Looped Reasoning Language Models

Hugh Blayney, Álvaro Arroyo, Johan Obando-Ceron, Pablo Samuel Castro, Aaron C. Courville, Michael M. Bronstein, Xiaowen Dong
April 13, 2026 Current Opinion in Structural Biology
Steering generative models for protein design: Aligning and conditioning strategies

Filippo Stocco, Michele Garibbo, Noelia Ferruz
Curated by Papers for Protein Design Using Deep Learning · 1. Reviews · 1.1 De novo protein design
April 11, 2026 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
Curated by Papers for Protein Design Using Deep Learning · 5.4 Transformer-based · 5.Function to Sequence
April 10, 2026 Nature Metabolism
iNOS modulates inflammatory responses in an NO-independent manner through direct interaction with IRG1 in mitochondria

Marina Diotallevi, Carlos Outeiral, Priyanka Patel, Gareth S. D. Purvis, Surawee Chuaiphichai, Thomas Nicol, Faseeha Ayaz, Daniel Allen Nissley, Ganna O. Krasnoselska, Svenja Hester, John H. McVey, Román Fischer, Benedikt Mathias Kessler, Charlotte Mary Deane, Raymond J. Owens, Keith M. Channon, Mark J. Crabtree
April 10, 2026 Biochemistry
AI-Designed Peptides as Tools for Biochemistry

Lauren Hong, Sophia Vincoff, Pranam Chatterjee
April 8, 2026 Nature Biotechnology
Sequence Display enables large-scale sequence–activity datasets for rapid protein evolution

Linqi Cheng, Xinzhe Zheng, Shiyu Jiang, Yu Hu, Y. N. Liu, Kaiqiang Yang, Jinyan Rui, Haoxue Ding, Mengxi Zhang, Teng Yuan, Qianglan Lu, Haoxin Leo Ye, C. Li, Yiming Guo, Zuotong Tian, Anna Qin, Boyang Zhou, Kevin Yang, Xiongyi Huang, Han Xiao
April 8, 2026 Zenodo (CERN European Organization for Nuclear Research)
CytED and test datasets for pyCytED

Lukas Oesinghaus, Molly Park, Rulin Shao, Pang Wei Koh, Georg Seelig
April 8, 2026 Zenodo (CERN European Organization for Nuclear Research)
Sampling antibody conformational ensembles with ABodyBuilder4-STEROIDS Dataset

King Ifashe, Fabian C. Spoendlin, Matteo Cagiada, Charlotte Mary Deane
April 6, 2026
Evolutionary transfer learning enables organism-wide inference of mammalian enhancer landscapes

Chengxiang Qiu, Riza M. Daza, Ian C. Welsh, Rupali P Patwardhan, Beth K. Martin, Tony W. Li, Shizhao Yang, Camiel C. A. Mannens, Seppe De Winter, Niklas Kempynck, Megan L. Taylor, Olivia Fulton, Truc-Mai Le, Diana R. O’Day, Jean‐Benoît Lalanne, Silvia Domcke, Stephen A. Murray, Stein Aerts, Cole Trapnell, Jay Shendure
April 6, 2026 arXiv (Cornell University)
How Well Do Agentic Skills Work in the Wild: Benchmarking LLM Skill Usage in Realistic Settings

Yujian Liu, Jiabao Ji, Li An, Tommi Jaakkola, Yang Zhang, Shiyu Chang
April 6, 2026 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
Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.2 Diffusion-based
April 6, 2026 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
Curated by Papers for Protein Design Using Deep Learning · 2. Model-based design · 2.1.1 trRosetta-based
April 4, 2026 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
Curated by Papers for Protein Design Using Deep Learning · 5.12 Diffusion-based · 5.Function to Sequence
April 3, 2026 Cancer Research
Abstract 5484: Designing ATP-gated proteins for tumor selective drug delivery.

Angela Mei, Azim M. Dharani, Jody Mou, Benjamin N. Fry, Nicholas F. Polizzi
April 2, 2026 Current Opinion in Structural Biology
AI-based methods for simulating, sampling, and predicting protein ensembles

Bowen Jing, Bonnie Berger, Tommi Jaakkola
April 1, 2026 Cell
Tackling the complexity of cancer with generative models

Ashley Mae Conard, Madeline Hughes, James Hall, Neil Tenenholtz, Eric Zimmermann, Lorin A. Crawford, Ava P. Amini, Kristen Severson
April 1, 2026 Bioinformatics
Protein FID: improved evaluation of protein structure generative models

Felix Faltings, Hannes Stark, Tommi Jaakkola, Regina Barzilay
April 1, 2026 Zenodo (CERN European Organization for Nuclear Research)
Universal Cell Embeddings provides a Foundation Model for Cell Biology

Yanay Rosen, Yusuf Roohani, Ayush Agrawal, Leon Samotorcan, Tabula Sapiens Consortium, Stephen R. Quake, Jure Leskovec
April 1, 2026 arXiv (Cornell University)
Online Reasoning Calibration: Test-Time Training Enables Generalizable Conformal LLM Reasoning

Cai Zhou, Zekai Wang, Menghua Wu, Qianyu Julie Zhu, Feng Shi, Chenyu Wang, Ashia Wilson, Tommi Jaakkola, Stephen Bates
March 31, 2026 Cell
Rational discovery of therapeutic PAK1 allosteric activators

Yu Hui He, James S.H. Bae, Elzbieta Nowak, Carlos Outeiral, Daniel Allen Nissley, Anthony Tumber, G. Berridge, E. Salah, Yi Wang, Wenqi He, Hongyuan Zhang, Tangting Chen, Samuel E. Tusk, Sebastian Mathea, Ying-Jie Wang, Alexander Grassam-Rowe, Philipp Kukura, Christopher John Schofield, Darragh Patrick O'Brien, Andrea Pierangelini, Grant C. Churchill, Thomas Lanyon‐Hogg, Yunbo Ke, Chao Xu, Tao Ye, Hugh C Watkins, Liming Ying, Andreas Koschinski, R John Solaro, X Tan, Jani Reddy Bolla, Xin Wang, Stefan Knapp, Charlotte Mary Deane, Manuela Zaccolo, Marcin Nowotny, Ming Lei
March 30, 2026 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
March 30, 2026 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
Curated by Papers for Protein Design Using Deep Learning · 3. Function to Scaffold · 3.5 RL-based
March 27, 2026 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
Curated by Papers for Protein Design Using Deep Learning · 7. Other tasks · 7.4 Framework
March 26, 2026 Scientific Reports
Description of a collaborative sperm whale birth and shifts in coda vocal styles during key events

Yaniv Aluma, Zethra Baron, Ricardo Barrett, Courtney Baumgartner, Gašper Beguš, Sushmita Bhattacharya, Michael M. Bronstein, Shlomi Dahan, Oscar Davis, Sarah de Haas, Jullan Defoe, Joseph DelPreto, Roberto Dessì, Roee Diamant, John Gatesy, Kevin George, Shane Gero, Darren Gibbons, Dean Gibbons, Stephanie Gil, Shafi Goldwasser, David F. Gruber, Odel Harve, Alyssa M. Hernandez, Mapal Ishay, Ninad Jadhav, Lakshyana KC, Aidan Kenny, Antonio Leitao, Maxime Lucas, Alaa Maalouf, Peter Malkin, Yaly Mevorach, Stefano Pagani, Orr Paradise, Giovanni Petri, Simone Poetto, Emanuele Rossi, Daniela L. Rus, Michael Salino-Hugg, Andrea Santoro, Pratyusha Sharma, Dan Tchernov, Antonio B. Torralba, Pernille Tønnesen, Daniel M. Vogt, Robert J. Wood
March 26, 2026 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
Curated by Papers for Protein Design Using Deep Learning · 7. Other tasks · 7.1 Effects of mutation & Fitness Landscape
March 25, 2026 Nature
Remembrance of inflammations past

Chengxiang Qiu, Jay Shendure
March 25, 2026 Stanford Digital Repository
Collaborative AI agents

Shirley Yingxin Wu, Jure Leskovec, James Zou, Diyi Yang, Stanford University. School of Engineering., Stanford University. Computer Science Department.
March 25, 2026 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
March 25, 2026 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
Curated by Papers for Protein Design Using Deep Learning · 7. Other tasks · 7.4 Framework
March 25, 2026 bioRxiv (Cold Spring Harbor Laboratory)
CombinGym: a benchmark platform for machine learning-assisted design of combinatorial protein variants

Yongcan Chen, Lihao Fu, Xuchao Lu, Wenzhuo Li, Yuan Gao, Yibo Wang, Zhicheng Ruan, Tong Si
Curated by Papers for Protein Design Using Deep Learning · 7. Other tasks · 7.1 Effects of mutation & Fitness Landscape
March 24, 2026 arXiv (Cornell University)
Can Graph Foundation Models Generalize Over Architecture?

Benjamin Gutteridge, Michael M. Bronstein, Xiaowen Dong
March 23, 2026 Journal of Chemical Information and Modeling
AssayMatch: Learning To Select Data for Molecular Activity Models

Vincent Fan, Regina Barzilay
March 19, 2026 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
Curated by Papers for Protein Design Using Deep Learning · 5.6 RL-based · 5.Function to Sequence
March 18, 2026 PLoS ONE
Computational design of functional random heteropolymers through atomistic simulations

Tianyi Jin, Collin S. Lung, Ting Xu, Connor W. Coley, Alfredo Alexander‐Katz
March 18, 2026 PLANT PHYSIOLOGY
AI-enabled protein design facilitates future plant research and crop breeding

Yuxuan Lou, Tianhao Wu, Fan Xia, Anwen Zhao, Xiangfeng Wang
Curated by Papers for Protein Design Using Deep Learning · 1. Reviews · 1.1 De novo protein design
March 16, 2026 Stanford Digital Repository
Drugs and where to find them : multi-scale artificial intelligence methods for identifying ligand-binding pockets and opioid-related social media posts

Kristy A. Carpenter, Russ Biagio Altman, Polly Morrell Fordyce, Jure Leskovec, Ying Lü, Stanford University. School of Medicine., Stanford University. Department of Biomedical Informatics.
March 16, 2026 bioRxiv (Cold Spring Harbor Laboratory)
Improved vector toolkit for genome writing in mammalian cells

Kelly Barriball, Brianna Berrios, Camila Coelho, Sudarshan Pinglay, Yu Zhao, Noor Chalhoub, Tiffany Tsou, John T. Atwater, Jef D. Boeke, Weimin Zhang, Ran Brosh
March 14, 2026 Zenodo (CERN European Organization for Nuclear Research)
Companion data for CytED construction software

Lukas Oesinghaus, Molly Park, Rulin Shao, Pang Wei Koh, Georg Seelig
March 14, 2026 Proceedings of the AAAI Conference on Artificial Intelligence
Advancing Protein Design via Multi-Agent Reinforcement Learning with Pareto-Based Collaborative Optimization

Mingming Zhu, Jiahua Rao, Xiaoyu Chen, Qianmu Yuan, Yuedong Yang
Curated by Papers for Protein Design Using Deep Learning · 2. Model-based design · 2.5 Sampling-algorithms
March 13, 2026 Stanford Digital Repository
Real-world causal inference for healthcare and public policy

Hamed Nilforoshan, Jure Leskovec, Emma Brunskill, Stefan Wager, Stanford University. School of Engineering., Stanford University. Computer Science Department.
March 9, 2026 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
Curated by Papers for Protein Design Using Deep Learning · 5.2 VAE-based · 5.Function to Sequence
March 5, 2026 ACS Central Science
Higher-Level Strategies for Computer-Aided Retrosynthesis

Jihye Roh, Joonyoung F. Joung, Kevin Yu, Zhengkai Tu, G. Logan Bartholomew, Omar A. Santiago-Reyes, Mun Hong Fong, Richmond Sarpong, Sarah E. Reisman, Connor W. Coley
March 5, 2026 bioRxiv (Cold Spring Harbor Laboratory)
Functional reorganization of motor cortex connectivity during learning

Kayvon Daie, Kyle Aitken, Márton Rózsa, Matthew S. Bull, Peter C. Humphreys, Ziheng Christina Wang, Lucas W. Kinsey, Mohit Kulkarni, Kimberly Stachenfeld, Maria K. Eckstein, Zeb L. Kurth-Nelson, Claudia Clopath A, Timothy Lillicrap, Matthew Botvinick, Matthew D. Golub, Ştefan Mihalaş, Karel Svoboda
March 5, 2026 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
Curated by Papers for Protein Design Using Deep Learning · 2. Model-based design · 2.4 LLM-based
March 5, 2026 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
March 4, 2026 Nature
Genome modelling and design across all domains of life with Evo 2

Garyk Brixi, Matthew G. Durrant, Jerome Ku, Mohsen Naghipourfar, Michael Poli, Gwanggyu Sun, Greg Brockman, Daniel Chang, Alison Fanton, Gabriel A. Gonzalez, Samuel H. King, David B. Li, Aditi T. Merchant, Eric Nguyen, Chiara Ricci-Tam, David W. Romero, Jonathan C. Schmok, Ali Taghibakhshi, Anton Vorontsov, Brandon Yang, Myra Deng, Liv Gorton, Nam‐Ky Nguyen, Nicholas K. Wang, Michael T. Pearce, Elana P. Simon, Etowah Adams, Zachary J. Amador, Euan Angus Ashley, Stephen A. Baccus, Haoyu Dai, Steven Dillmann, Stefano Ermon, Daniel Guo, Michael H. Herschl, Rajesh Ilango, Ken Janik, Amy X. Lu, Reshma Mehta, Mohammad R. K. Mofrad, Madelena Y. Ng, Jaspreet Pannu, Christopher Ré, John St. John, Jeremy Sullivan, Joseph Tey, Ben T Viggiano, Kevin Zhu, Gregory J. Zynda, Daniel Balsam, Patrick Collison, Anthony B. Costa, Tina Hernandez‐Boussard, Eric Ho, Mingyu Liu, Thomas McGrath, Kimberly Powell, Sudarshan Pinglay, Dave P. Burke, Hani Goodarzi, Patrick D. Hsu, Brian Hie
March 4, 2026 ChemRxiv
Grand Challenges for Predictive Modeling in Small Molecule Drug Discovery

Connor W. Coley, Pankaj Daga, Marco De Vivo, Willem Jespers, Ashutosh S. Jogalekar, S Roy Kimura, Lucien Koenekoop, Anne‐Grete Märtson, Timothy R. Newhouse, Soumya Ray, Riccardo Sabatini, David C Thompson, Woody Sherman
March 4, 2026 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
Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.6 Transformer-based
March 3, 2026 arXiv (Cornell University)
Deep learning-guided evolutionary optimization for protein design

Erik Hartman, Di Tang, Johan A. Malmström
Curated by Papers for Protein Design Using Deep Learning · 7. Other tasks · 7.1 Effects of mutation & Fitness Landscape
March 2, 2026 arXiv (Cornell University)
PanCanBench: A Comprehensive Benchmark for Evaluating Large Language Models in Pancreatic Oncology

Yimin Zhao, Sheela Damle, Simone E. Dekker, Scott Geng, Karly Williams Silva, Jesse J. Hubbard, Manuel Fernández, Fatima Zelada-Arenas, Alejandra Alvarez, Brianne Flores, Alexis Rodriguez, Stephen M. Salerno, Carrie Wright, Zihao Wang, Pang Wei Koh, Jeffrey T. Leek
March 2, 2026 PubMed
Branched Schrödinger Bridge Matching.

Sophia Tang, Yinuo Zhang, Alexander Tong, Pranam Chatterjee
March 2, 2026 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
Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.8 Flow-based
March 1, 2026 Nature Methods
AF2BIND: predicting small-molecule binding sites using the pair representation of AlphaFold2

Artem Gazizov, Anna Lian, Casper A. Goverde, Jody Mou, Sergey Ovchinnikov, Nicholas F. Polizzi
March 1, 2026 IEEE Conference on Secure and Trustworthy Machine Learning (SaTML)
A False Sense of Privacy: Evaluating Textual Data Sanitization Beyond Surface-level Privacy Leakage

Rui Xin, Niloofar Mireshghallah, Shuyue Stella Li, Michael Duan, Hyunwoo Kim, Yejin Choi, Yulia Tsvetkov, Sewoong Oh, Pang Wei Koh
March 1, 2026 The Lancet Digital Health
Bridging the gap: aligning clinical decision support regulation with clinical practice in the era of artificial intelligence

Maëlle-Marie Corso, Paul T Kim, Brenna T. Loufek, Leslie R. Lamb, Regina Barzilay
March 1, 2026 Cell Reports Methods
Scalable nonparametric clustering with unified marker gene selection for single-cell RNA-seq data

Chibuikem Chukwudalu Nwizu, Madeline Hughes, Michelle L. Ramseier, Andrew W. Navia, Alex K. Shalek, Nicolò Fusi, Srivatsan Raghavan, Peter S. Winter, Ava P. Amini, Lorin A. Crawford
March 1, 2026 Computational and Structural Biotechnology Journal
BioPipelines: Accessible Computational Protein and Ligand Design for Chemical Biologists

Gianluca Quargnali, Pablo Rivera‐Fuentes
Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.3 RoseTTAFold-based
March 1, 2026 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
Curated by Papers for Protein Design Using Deep Learning · 1. Reviews · 1.1 De novo protein design
March 1, 2026 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
Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.8 Flow-based
February 24, 2026 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
February 24, 2026 bioRxiv (Cold Spring Harbor Laboratory)
Beyond alignment: synergistic integration is required for multimodal cell foundation models

Till Richter, Eric Zimmermann, James Hall, Fabian Joachim Theis, Srivatsan Raghavan, Peter S. Winter, Ava P. Amini, Lorin A. Crawford
February 24, 2026 arXiv (Cornell University)
Zatom-1: Towards a Multimodal Foundation Model for 3D Molecules and Materials

Alex Morehead, Miruna Cretu, Antonia Panescu, Rishabh Anand, Maurice Weiler, Tynan J. Perez, Samuel M. Blau, Steven Farrell, W. Bhimji, Anubhav Jain, Hrushikesh P. Sahasrabuddhe, Pietro Lio, Tommi Jaakkola, Rafael Gómez‐Bombarelli, Rex Ying, N. Benjamin Erichson, Michael W. Mahoney
February 24, 2026 Angewandte Chemie
A Chemoselective and Stereodivergent Platform of Heme‐Nitrene Transferases to Access Chiral Aryl‐β‐Amino Esters and An Investigation of the Sequence‐Activity Landscape

Julia C. Reisenbauer, Hayden M. Carder, Ariane Mora, Ana Jaramillo, Frances H. Arnold
February 23, 2026 Annual Review of Analytical Chemistry
The Next Generation of Protein Sequencing and Analysis Methods

K. C. Wong, Mattias Tolhurst, Oren A. Fox, Safwan Diwan, Nicholas Bogard, Jeff Nivala
February 23, 2026 arXiv (Cornell University)
PackFlow: Generative Molecular Crystal Structure Prediction via Reinforcement Learning Alignment

Akshay Subramanian, Elton Pan, Juno Nam, Maurice Weiler, Shuhui Qu, Cheol Woo Park, Tommi Jaakkola, Elsa Olivetti, Rafael Gómez‐Bombarelli
February 22, 2026 mAbs
2025 Ginkgo Datapoints Antibody Developability Competition outcomes: limited model performance and a call for data standardization

Lood van Niekerk, Joshua Moller, Seth Ritter, Porfirio Quintero-Cadena, Rich Cohen, Georgia Channing, Michael Chungyoun, Laura M. Rand, Alexander Smith, Aanal Bhatt, Yolaine Pierre, Blake Harris, Xiang Ao, Lucía Daniela Grippo, Maximilian Schwenk, Adam Rosenbaum, Olga Allen, Nimra Asi, Jiang Zhu, Aviral Singh, Daksh Sammi, Rushikesh Jadhav, Antonín Dušek, Shyam Chandra, Valentin Badea, Nels Thorsteinson, Nathaniel Blalock, Jeonghyeon Kim, Oliver M. Turnbull, Ameya Kulkarni, Vivek Kohar, Netsanet Gebremedhin, Charlotte Mary Deane, Peter M. Tessier, Ammar Arsiwala
February 22, 2026 bioRxiv (Cold Spring Harbor Laboratory)
Reprogramming CAR T-Cells with designed bioPROTACs

Vivek S. Peche, Sebastian Kenny, Tae Gun Kang, Brian Coventry, Tian Mi, Inna Goreshnik, Mariana Garcia Sanchez, Reid Martin, Macey Smith, Dionne K. Vafeados, Rahul S. Kathayat, Yu Kaiwen, Zuo-Fei Yuan, Long Wu, Anthony A. High, Andrew N. Nemecek, Elizabeth Wickman, Adeleye Oluwatosin Adeshakin, Francesca Ferrara, Robert E. Throm, Taosheng Chen, Ben Youngblood, David A. Baker, Stephen M Gottschalk
Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.3 RoseTTAFold-based
February 21, 2026 Communications Biology
LICHEN enables light-chain immunoglobulin sequence generation conditioned on the heavy chain and experimental needs

Henriette Capel, Isaac Ellmen, Chris J. Murray, Giulia Mignone, Megan Black, Brendan Clarke, Conor Breen, Sean Tierney, Patrick Dougan, Richard J. Buick, Alexander Greenshields‐Watson, Charlotte Mary Deane
February 20, 2026 Cell Genomics
A multiplex, prime editing framework for identifying drug resistance variants at scale

Florence M.C. Abadie, Chase C. Suiter, Nahum T. Smith, Riza M. Daza, Mary C Rominger, Phoebe C. R. Parrish, Troy A. McDiarmid, Jean‐Benoît Lalanne, Beth Martin, Diego Calderon, Amira Ellison, Sitapriya Moorthi, Jay Shendure, Lea M. Starita
February 19, 2026 Science
Rapid directed evolution guided by protein language models and epistatic interactions

Vincent Q. Tran, Matthew Nemeth, Liam J. Bartie, Sita S. Chandrasekaran, Alison Fanton, Hyungseok C. Moon, Brian Hie, Silvana Konermann, Patrick D. Hsu
February 18, 2026 Current Opinion in Structural Biology
Moving the antibody: Molecular dynamics for molecular mechanisms and developability

Matteo Cagiada, Charlotte Mary Deane
February 18, 2026 medRxiv
Revised estimates of the types and durations of long Covid symptoms based on claims records from 245 Million US patients

Hamed Nilforoshan, Julia Reisler, Erfan Jahanparast, Michael Moor, Steven N. Goodman, Stefan Wager, Jure Leskovec
February 17, 2026 ACM eBooks
ACM TechBrief: Buy versus Build an LLM

Joan Lu, Ziwei Xu, William Chandra Tjhi, Junnan Li, Antoine Bosselut, Pang Wei Koh, Mohan Kankanhalli
February 17, 2026 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
Curated by Papers for Protein Design Using Deep Learning · 5.7 Flow-based · 5.Function to Sequence
February 17, 2026 bioRxiv (Cold Spring Harbor Laboratory)
Hierarchical latent representations reveal protein organization for functional discovery and design

Zhengyang Guo, Zi Wang, Shimin Wang, Yongping Chai, Kaiming Xu, Ming Li, Wei Li, Guangshuo Ou
Curated by Papers for Protein Design Using Deep Learning · 7. Other tasks · 7.1 Effects of mutation & Fitness Landscape
February 16, 2026 arXiv (Cornell University)
Rethinking Diffusion Models with Symmetries through Canonicalization with Applications to Molecular Graph Generation

Cai Zhou, Zijie Chen, Zian Li, Jike Wang, Kaiyi Jiang, Li, Pan, Rose Yu, Muhan Zhang, Stephen Bates, Tommi Jaakkola
February 16, 2026 arXiv (Cornell University)
Cold-Start Personalization via Training-Free Priors from Structured World Models

Avinandan Bose, Shuyue Stella Li, Faeze Brahman, Pang Wei Koh, Simon S. Du, Yulia Tsvetkov, Maryam Fazel, Lin Xiao, Asli Celikyilmaz
February 16, 2026 arXiv (Cornell University)
MacroGuide: Topological Guidance for Macrocycle Generation

Alicja W. Maksymiuk, Alexandre Duplessis, Michael M. Bronstein, Alexander Tong, Fernanda Santos Duarte, İsmail İlkan Ceylan
February 14, 2026 arXiv (Cornell University)
ALMo: Interactive Aim-Limit-Defined, Multi-Objective System for Personalized High-Dose-Rate Brachytherapy Treatment Planning and Visualization for Cervical Cancer

Edward Chen, Natalie Dullerud, Pang Wei Koh, Thomas R Niedermayr, Elizabeth A. Kidd, Sanmi Koyejo, Carlos Guestrin
February 13, 2026 arXiv (Cornell University)
RelBench v2: A Large-Scale Benchmark and Repository for Relational Data

Justin Gu, Rishabh Ranjan, Charilaos I. Kanatsoulis, Haiming Tang, Martin Jurkovic, Valter Hudovernik, Mark Znidar, Pranshu Chaturvedi, Parth Shroff, Li, Fengyu, Jure Leskovec
February 13, 2026 arXiv (Cornell University)
Buy versus Build an LLM: A Decision Framework for Governments

Jiahao Lu, Ziwei Xu, William Tjhi, Junnan Li, Antoine Bosselut, Pang Wei Koh, Mohan Kankanhalli
February 12, 2026 Nature Catalysis
A geometric foundation model for enzyme retrieval with evolutionary insights

Yong Liu, Chenqing Hua, Menglong Xu, Tao Zeng, Jiahua Rao, Zhongyue Zhang, Rongjie Wu, Jing‐Ke Weng, Connor W. Coley, Shuangjia Zheng
February 12, 2026 Zenodo (CERN European Organization for Nuclear Research)
Data and Model for Quantifying the Failure Modes of Current One-step Retrosynthesis Models

Suong B. A. Tran, Jihye Roh, Connor W. Coley
February 12, 2026 arXiv (Cornell University)
Categorical Flow Maps

Daan Roos, Oscar Davis, Floor Eijkelboom, Michael M. Bronstein, Max Welling, İsmail İlkan Ceylan, Luca Ambrogioni, Jan-Willem van de Meent
February 11, 2026 Angewandte Chemie International Edition
Lysine Targeting Group‐Transfer Chimeras for Proximity Induction

Sameek Singh, Kien Tran, Endri Karaj, Basudeb Mondal, Wenzhi Tian, Surached Siriwongsup, Shaimaa H. Sindi, Uttam Dhawa, Kaushik Pal, Veronika M. Shoba, Sunny Shi, Anna Lian, Jody Mou, Myeonghoon Han, Prashant R. Singh, Nicholas F. Polizzi, Amit Choudhary
February 11, 2026 Nature Protocols
Multichannel genomic recording of biological information with ENGRAM

Jenny F. Nathans, Troy A. McDiarmid, Wei Chen, Jay Shendure
February 10, 2026 arXiv (Cornell University)
Predictive Query Language: A Domain-Specific Language for Predictive Modeling on Relational Databases

Vid Kocijan, Jinu Sunil, Jan Eric Lenssen, Viman Deb, Xinwei Xe, Federico Reyes Gomez, Matthias Fey, Jure Leskovec
February 9, 2026 PLoS Computational Biology
Trainable subnetworks reveal insights into structure knowledge organization in protein language models

Ria Vinod, Ava P. Amini, Lorin A. Crawford, Kevin Yang
February 9, 2026 Nature Communications
Author Correction: Random access and semantic search in DNA data storage enabled by Cas9 and machine-guided design

Carina E. Imburgia, Lee Organick, Karen Huilin Zhang, Nicolás Cardozo, Jeff McBride, Callista Bee, Delaney Wilde, Gwendolin Roote, Sofia Jorgensen, David Ward, Charlie Anderson, Karin Strauß, Luís Ceze, Jeff Nivala
February 7, 2026 arXiv (Cornell University)
Generative structural elucidation from mass spectra as an iterative optimization problem

Mrunali Manjrekar, Runzhong Wang, Samuel Goldman, Jenna C. Fromer, Connor W. Coley
February 7, 2026 arXiv (Cornell University)
HumanLM: Simulating Users with State Alignment Beats Response Imitation

Wu, Shirley, Evelyn Choi, Arpandeep Khatua, Zhanghan Wang, Joy He-Yueya, Tharindu Cyril Weerasooriya, Wei Wei, Diyi Yang, Jure Leskovec, James Zou
February 6, 2026 Zenodo (CERN European Organization for Nuclear Research)
Auxiliary datasets for Generative structural elucidation from mass spectra as a iterative optimization problem

Mrunali Manjrekar, Runzhong Wang, Samuel Goldman, Jenna C. Fromer, Connor W. Coley
February 6, 2026 arXiv (Cornell University)
Anchored Decoding: Provably Reducing Copyright Risk for Any Language Model

Jacqueline He, Jonathan Hayase, Wen-tau Yih, Sewoong Oh, Luke Zettlemoyer, Pang Wei Koh
February 6, 2026 arXiv (Cornell University)
SaDiT: Efficient Protein Backbone Design via Latent Structural Tokenization and Diffusion Transformers

Mo, Shentong, Lanqing Li
Curated by Papers for Protein Design Using Deep Learning · 3. Function to Scaffold · 3.4 Diffusion-based
February 5, 2026 Macromolecules
Energy Landscape and Stability in Random Heteropolymers: Somewhere Between Protein Folding and Plastic Miscibility

Tianyi Jin, Connor W. Coley, Alfredo Alexander‐Katz
February 5, 2026 arXiv (Cornell University)
Diamond Maps: Efficient Reward Alignment via Stochastic Flow Maps

Peter Holderrieth, Douglas Chen, Luca Eyring, Ishin Shah, Giri Anantharaman, Yutong He, Zeynep Akata, Tommi Jaakkola, Nicholas M. Boffi, Max Simchowitz
February 5, 2026 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
Curated by Papers for Protein Design Using Deep Learning · 4.5 GNN-based · 4.Scaffold to Sequence
February 4, 2026 Nature
Synthesizing scientific literature with retrieval-augmented language models

Akari Asai, Jacqueline He, Rulin Shao, Weijia Shi, Amanpreet Singh, Joseph Chee Chang, Kyle Lo, Luca Soldaini, Sergey Feldman, Mike D’Arcy, David Wadden, Matt Latzke, Jenna Sparks, Jena D. Hwang, Varsha Kishore, Minyang Tian, Pan Ji, Shengyan Liu, Hao Tong, Bohao Wu, Yanyu Xiong, Luke Zettlemoyer, Graham Neubig, Daniel S. Weld, Doug Downey, Wen-tau Yih, Pang Wei Koh, Hannaneh Hajishirzi
February 4, 2026 arXiv (Cornell University)
Turbulence teaches equivariance to neural networks

Ryley McConkey, Julia Balla, Bailey, Jeremiah, Ali Backour, E. Hofgard, Tommi Jaakkola, Abigail S. Bodner, Tess Smidt
February 4, 2026 arXiv (Cornell University)
Reliable and Responsible Foundation Models: A Comprehensive Survey

Xinyu Yang, Junlin Han, Rishi Bommasani, Jinqi Luo, Wenjie Qu, Wangchunshu Zhou, Adel Bibi, Xiyao Wang, Jaehong Yoon, Elias Stengel-Eskin, Shengbang Tong, Lingfeng Shen, Rafael Rafailov, Runjia Li, Zhaoyang Wang, Yiyang Zhou, Chenhang Cui, Yu Wang, Wenhao Zheng, Huichi Zhou, Jindong Gu, Zhaorun Chen, Peng Xia, Tony Lee, Thomas P. Zollo, Vikash Sehwag, Jixuan Leng, Jiuhai Chen, Yuxin Wen, Huan Zhang, Zhun Deng, Linjun Zhang, Pavel Izmailov, Pang Wei Koh, Yulia Tsvetkov, Andrew Wilson, Jiaheng Zhang, James Zou, Cihang Xie, Hao Wang, Philip H.S. Torr, Julian McAuley, David Alvarez-Melis, Florian Tramèr, Kaidi Xu, Suman Jana, Chris Callison-Burch, René Vidal, Filippos Kokkinos, Mohit Bansal, Beidi Chen, Huaxiu Yao
February 4, 2026 arXiv (Cornell University)
Protein Autoregressive Modeling via Multiscale Structure Generation

Yanru Qu, Cheng-Yen Hsieh, Zaixiang Zheng, Ge Liu, Quanquan Gu
Curated by Papers for Protein Design Using Deep Learning · 3. Function to Scaffold · 3.8 Autoregressive
February 4, 2026 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
Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.3 RoseTTAFold-based
February 3, 2026 arXiv (Cornell University)
PluRel: Synthetic Data unlocks Scaling Laws for Relational Foundation Models

Vignesh Kothapalli, Ranjan, Rishabh, Valter Hudovernik, Vijay Prakash Dwivedi, Johannes Hoffart, Carlos Guestrin, Jure Leskovec
February 3, 2026 arXiv (Cornell University)
Privasis: Synthesizing the Largest "Public" Private Dataset from Scratch

Hyunwoo Kim, Niloofar Mireshghallah, Michael Duan, Rui Xin, Shuyue Stella Li, Jaehun Jung, David Acuna, Qi Pang, Hanshen Xiao, G. Edward Suh, Sewoong Oh, Yulia Tsvetkov, Pang Wei Koh, Yejin Choi
February 3, 2026 arXiv (Cornell University)
Generative AI for Enzyme Design and Biocatalysis

Lasse Middendorf, Noelia Ferruz
Curated by Papers for Protein Design Using Deep Learning · 1. Reviews · 1.5 Enzyme design
February 2, 2026 arXiv (Cornell University)
FragmentFlow: Scalable Transition State Generation for Large Molecules

Ron Shprints, Peter Holderrieth, Juno Nam, Rafael Gómez‐Bombarelli, Tommi Jaakkola
February 2, 2026 Stanford Digital Repository
Generative AI for drug design : methods and applications

Kyle Swanson, Anshul Bharat Kundaje, James Zou, Jure Leskovec, Stanford University. School of Engineering., Stanford University. Computer Science Department.
February 2, 2026 npj Women s Health
Publisher Correction: Identifying nutraceutical targets to treat polycystic ovary syndrome using graph representation learning

Simon Hanassab, Joshua Southern, Ayomide Victoria Olabode, Ivan Laponogov, Michael M. Bronstein, Alexander N. Comninos, Thomas Heinis, Ali Abbara, Chioma N. Izzi‐Engbeaya, Kirill Veselkov, Waljit Singh Dhillo
February 2, 2026 bioRxiv (Cold Spring Harbor Laboratory)
A unified pipeline for discovering previously unknown enzyme activities

Ariane Mora, Julia C. Reisenbauer, Helen Schmid, Ikumi Miyazaki, Yueming Long, Jason Yang, Ryen L. O’Meara, Frances H. Arnold
February 1, 2026 Biophysical Journal
BPS2026 – AF2chi: Predicting protein side-chain rotamer distributions with AlphaFold2

Matteo Cagiada, Emil Thomasen, Sergey Ovchinnikov, Charlotte Mary Deane, Kresten Lindorff‐Larsen
January 31, 2026 Communications Biology
Characterising nanobody developability to improve therapeutic design using the Therapeutic Nanobody Profiler

Gemma L. Gordon, João Henrique Diniz Brandão Gervásio, Colby Souders, Charlotte Mary Deane
January 30, 2026 Nature Computational Science
Improving atlas-scale single-cell annotation models with hierarchical cross-entropy loss

Sebastiano Cultrera di Montesano, Davide D’Ascenzo, Srivatsan Raghavan, Ava P. Amini, Peter S. Winter, Lorin A. Crawford
January 30, 2026 bioRxiv (Cold Spring Harbor Laboratory)
Principles of in situ protein sequencing: expansion microscopy-adapted Edman degradation and amino acid recognition

Camille Marie Mitchell, Sara Z. Tavana, Joanne Peng, Hao Wang, Jiuhan Shi, Chi Zhang, Lilia Evgeniou, Masy Domecillo, Shiwei Wang, Daniel Estandian, Alexi G. Choueiri, E. Wong, Sarah Dohadwala, Isken Kenzhebaev, Tay Won Shin, Nicholas F. Polizzi, Laura L. Kiessling, Edward S. Boyden
January 30, 2026 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
Curated by Papers for Protein Design Using Deep Learning · 4.5 GNN-based · 4.Scaffold to Sequence
January 29, 2026 arXiv (Cornell University)
Minimal-Action Discrete Schrödinger Bridge Matching for Peptide Sequence Design

Shrey Goel, Pranam Chatterjee
January 29, 2026 arXiv (Cornell University)
ProDCARL: Reinforcement Learning-Aligned Diffusion Models for De Novo Antimicrobial Peptide Design

Fang Sheng, Mohammad Noaeen, Zahra Shakeri
Curated by Papers for Protein Design Using Deep Learning · 4.12 RL-based · 4.Scaffold to Sequence
January 28, 2026 arXiv (Cornell University)
Improving Diffusion Language Model Decoding through Joint Search in Generation Order and Token Space

Yi Shen, Tianjian Feng, Jiaqi Han, Wen Wang, Tianlang Chen, Chunhua Shen, Jure Leskovec, Stefano Ermon
January 26, 2026 bioRxiv (Cold Spring Harbor Laboratory)
ProChoreo: de novo Binder Design from Conformational Ensembles with Generative Deep Learning

Saisai Ding, Yi Zhang
Curated by Papers for Protein Design Using Deep Learning · 5.10 Autoregressive-models · 5.Function to Sequence
January 23, 2026 bioRxiv (Cold Spring Harbor Laboratory)
TCRAD: An End-to-End Framework for Antigen-Targeted T Cell Receptor Design

Chenao Li, Yaochi Guo, Xin Guan, Hui Chen, Yong Zhang, Pengyuan Yang, Jizhong Lou
Curated by Papers for Protein Design Using Deep Learning · 5.4 Transformer-based · 5.Function to Sequence
January 20, 2026 Bioinformatics
De novo protein–ligand design including protein flexibility and conformational adaptation

Jakob Agamia, Martin Zacharias
Curated by Papers for Protein Design Using Deep Learning · 2. Model-based design · 2.1.1 trRosetta-based
January 16, 2026 Proceedings of the National Academy of Sciences
Predicting epistasis across proteins by structural logic

Michelle Tang, Gareth A. Cromie, Anowarul Kabir, Martin S. Timour, Julee Ashmead, Russell S. Lo, Nathaniel Corley, Frank DiMaio, Hiroki Morizono, Ljubica Caldovic, Nicholas Ah Mew, Andrea Lynne Gropman, Amarda Shehu, Aimée M. Dudley
January 16, 2026 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, Gu, Lin, Jinhao Bi, Yingying Zhu
Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.4 CNN-based
January 14, 2026 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
Curated by Papers for Protein Design Using Deep Learning · 4.5 GNN-based · 4.Scaffold to Sequence
January 14, 2026 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, David A. 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
January 8, 2026 Cancer Cell
The ADAPT learning cancer treatment system: ARPA-H’s initiative to revolutionize cancer therapy

Andrea H. Bild, Michelle Cook Sangar, Jasmine A. McQuerry, Trey E. Ideker, Scott Kopetz, Lisa Carey, Aritro Nath, Daniel Marcus, Allison Regier, Naim Rashid, Regina Barzilay, Eric P. Winer, Ravi Salgia, Jyoti Dhar Malhotra, Andrew J. Gentles, Kenneth H. Buetow, Faisal Mahmood, David W. Markman, James A. Eddy, Michelle Afkhami, Kristin D. Alfaro-Munoz, Salvador Alonso, Kate Alpert, Jesús Anampa, Vineet Bafna, Marija Balić, Justin Micah Balko, Regina Barzilay, Stephen Bates, Tanios Bekaii‐Saab, Vincent Bernard, Andrea H. Bild, Genevieve Marie Boland, Mitesh J. Borad, Kenneth H. Buetow, Loren Buhle, Robyn Burns, Timothy Lewis Cannon, Lisa Carey, Luca F. Castelnovo, Ruizhe Chen, Mary E. Cianfrocca, Amy Sanders Clark, Ryan Bruce Corcoran, Annie Delores, Nicholas S. Duesbery, Georges El Fakhri, Ahmed M. Elkhanany, Stephanie Forrest, Paul Henry Frankel, Ignacio Fuentes, Justin F. Gainor, Andrew J. Gentles, Manju George, Olivier Gevaert, Karthik Giridhar, Jason I. Griffiths, Benjamin Haibe‐Kains, Stanley R. Hamilton, Nicole Herrera, Susan Galloway Hilsenbeck, Frederick Howard, David S. Hsu, Stephanie Huang, Laura A. Huppert, Trey E. Ideker, Claudine J. Isaacs, Leila V. Kiefer, Erin Kelly, Edward J. Kim, Scott Kopetz, Nevan J. Krogan, Ian E. Krop, Manfred Laubichler, Long Le, Adrian V. Lee, Heewook Lee, Su‐In Lee, Xiaochen Li, Christopher Hanyoung Lieu, NU Lin, Faisal Mahmood, Anirban Maitra, Carlo C. Maley, Jyoti Dhar Malhotra, David Managadze, Daniel Marcus, Maurie Markman, Dipen Maheshbhai Maru, Jasmine McQuerry, David G. Menter, Wells A. Messersmith, Mark Messervy, Jonathan D. Mizrahi, Van Karlyle Morris, Remya Nair, Rita Nanda, Aritro Nath, Tia Newgen, Kimmie Ng
January 8, 2026 arXiv (Cornell University)
Surface-based Molecular Design with Multi-modal Flow Matching

Fang Wu, Zhengyuan Zhou, Shuting Jin, Xiangxiang Zeng, Jure Leskovec, Jinbo Xu
January 7, 2026 bioRxiv (Cold Spring Harbor Laboratory)
AptaBLE: A Deep Learning Platform for Aptamer Generation and Analysis

Sawan Patel, Keith Fraser, Dhanush Gandavadi, Abhisek Dwivedy, Xing Wang, Fred Zhangzhi Peng, Pranam Chatterjee, Sherwood Yao
January 6, 2026 Nature Communications
Deep learning guided design of protease substrates

Carmen Martin-Alonso, Sarah Alamdari, Tahoura S. Samad, Kevin Yang, Sangeeta N. Bhatia, Ava Amini
January 6, 2026 Underline Science Inc.
Learning Inter-Atomic Potentials without Explicit Equivariance

Association for Artificial Intelligence 2026, Samuel M. Blau, Michael M. Bronstein, Ahmed A. Elhag, Alex Morehead, Garrett M. Morris, Arun Raja
January 6, 2026 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
Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.2 Diffusion-based
January 2, 2026 eLife
Squidly: Enzyme Catalytic Residue Prediction Harnessing a Biology-Informed Contrastive Learning Framework

William JF Rieger, Mikael Bodén A, Frances H. Arnold, Ariane Mora
January 2, 2026 Frontiers in Immunology
Pox-AbDab: the orthopoxvirus antibody database

Henriette Capel, Eric Ji Da Wang, Ben H. Williams, Charlotte Mary Deane, Matthew I. J. Raybould
January 2, 2026
Author response: Squidly: Enzyme Catalytic Residue Prediction Harnessing a Biology-Informed Contrastive Learning Framework

William JF Rieger, Mikael Bodén A, Frances H. Arnold, Ariane Mora
January 2, 2026
Reviewer #2 (Public review): Squidly: Enzyme Catalytic Residue Prediction Harnessing a Biology-Informed Contrastive Learning Framework

William JF Rieger, Mikael Bodén A, Frances H. Arnold, Ariane Mora
January 2, 2026
Reviewer #1 (Public review): Squidly: Enzyme Catalytic Residue Prediction Harnessing a Biology-Informed Contrastive Learning Framework

William JF Rieger, Mikael Bodén A, Frances H. Arnold, Ariane Mora
January 1, 2026 Cell
Mammalian genome writing: Unlocking new length scales for genome engineering

Sudarshan Pinglay, John T. Atwater, Ran Brosh, Jay Shendure, Matthew T. Maurano, Jef D. Boeke
January 1, 2026 Chemical Science
Black-box data: a new paradigm for biomedicine in the AI era

Luca Naef, Michael M. Bronstein
January 1, 2026 Chemical Society Reviews
An overview of reaction outcome prediction with physics-based and data-driven methods

Joonyoung F. Joung, Nicholas Casetti, Priyanka Raghavan, Connor W. Coley
January 1, 2026 Protein Engineering Design and Selection
Protein engineering: status report

Hui‐wang Ai, Frances H. Arnold, Doug Barrick, Hagan Bayley, Alfie-Louise R. Brownless, Robert E. Campbell, Roger Castells‐Graells, Pimchai Chaiyen, Roberto A. Chica, Lauren O. Chisholm, Daniel Christ, Guo-Chao Chu, Michael Chungyoun, Vincent G. H. Eijsink, Michael B. Elowitz, Douglas J. Fansher, Rudi Fasan, Gabriel Foley, Michelle S. Frei, Andreas Gagsteiger, Ruiyan Gao, Elizabeth M. J. Gillam, Jeffrey J. Gray, Luis F. Guerra, Birte Höcker, Zhiyang Jin, Shina Caroline Lynn Kamerlin, Nobuyasu Koga, Roland E. Kontermann, Brian A. Kuhlman, O Langlois, Dongyang Li, Roberto Dias Lins, Chang C. Liu, Lu Liu, Diego López Barreiro, Peilong Lu, Sohum Mehta, Ikumi Miyazaki, Manuel M. Müller, Serge Muyldermans, Naoto Nemoto, Jeff Nivala, James K. Nuñez, Izaiah J. Ornelas, Joelle N. Pelletier, Andreas Plückthun, Owen T. Porth, Kridsadakorn Prakinee, Yujia Qing, Julia C. Reisenbauer, Sandy Schmidt, Oliver Seifert, Mikhail G. Shapiro, Rachna Sharma, Nilmani Singh, Benjamin J. Smith, Jamie B. Spangler, Rie Koga, Takuya Terai, Henrik Terholsen, Mattias Tolhurst, Katherine W. Tripp, Vanessa Tanja Trossmann, Chandra L. Tucker, Onur Turak, James A. Van Deventer, Anikó Várnai, Isabelle F. T. Viana, Amy M. Weeks, Karl Dane Wittrup, K. C. Wong, Chenggang Xi, Todd O. Yeates, Andy Hsien-Wei Yeh, Jin Zhang, Tiger Zhang, Huimin Zhao, Fang Zheng, Jingyi Zhu, Sacha Zinn
January 1, 2026 Chemical Science
Quantifying the failure modes of current one-step retrosynthesis models

Suong B. A. Tran, Jihye Roh, Connor W. Coley
January 1, 2026 IEEE Transactions on Signal Processing
On the Impact of Sample Size in Reconstructing Noisy Graph Signals: A Theoretical Characterisation

Baskaran Sripathmanathan, Xiaowen Dong, Michael M. Bronstein
January 1, 2026 Neurotrauma Reports
Ten-Year Latent Trajectories of Global Function and Their Associations with Social Relationship Factors: A Traumatic Brain Injury Model Systems Study

Evan D. Feigel, Michael J. Mastrodicasa, Charlotte B. Luster, Brenna Finegan, David Guo, Chris W. Lewis, Maëlle-Marie Troadec, Ben Olsen, Ignacio Fuentes, Joseph T. Giacino, Regina Barzilay, Daniel Hamed Daneshvar
January 1, 2026 Chemical Science
A machine learning-based workflow for transaminase selection

Alexander J. Rago, Priyanka Raghavan, Lisandra Santiago-Capeles, Ruijie Zhang, Y Wang, Connor W. Coley
January 1, 2026 Daedalus
AI & the Discovery of Molecules through Autonomous Laboratories

Connor W. Coley
January 1, 2026 Zenodo (CERN European Organization for Nuclear Research)
Data - Generating Hybrid Proteins with the MSA-Transformer

Sanjana Tule, Samuel J. Davis, Ivan Koludarov, Ariane Mora, Mikael Bodén A
January 1, 2026 Neurotrauma Reports
Distinct Five-Year Latent Class Trajectories and Predictors of Functional Cognitive Independence Following Traumatic Brain Injury: A TBI Model Systems Study

Evan D. Feigel, Charlotte B. Luster, Chris W. Lewis, Brenna Finegan, Michael J. Mastrodicasa, Maëlle-Marie Troadec, David Guo, Ben Olsen, Ignacio Fuentes, Joseph T. Giacino, Regina Barzilay, Daniel Hamed Daneshvar
January 1, 2026 Chemical Science
Syndirella: synthesis-directed fragment elaboration enables extensive and cost-effective binding site exploration beyond catalog compounds

Kate K. Fieseler, Max Winokan, Joseph Morrone, Charlotte Mary Deane, Frank von Delft, Warren Athol Thompson
January 1, 2026 Science
De novo design of small molecule–regulated protein oligomers

Qihan Jin, Yukai Wang, Dachuan Chen, Jinyang Liao, Zhanyuan Cui, Yuxuan Fan, An‐Ping Zeng, Mingqi Xie, Longxing Cao
Curated by Papers for Protein Design Using Deep Learning · 4.5 GNN-based · 4.Scaffold to Sequence
January 1, 2026 Bioinformatics Advances
Computational design of class II MHC binding peptide with sequence-based evolution information

Ying Cao, Yuqing Li, Weitong Ren, Wenfei Li, Ming Yang
Curated by Papers for Protein Design Using Deep Learning · 5.4 Transformer-based · 5.Function to Sequence
January 1, 2026 Digital Discovery
CyclicMPNN: stable cyclic peptide sequence generation

Andrew C. Powers, Yanapat Janthana, Parisa Hosseinzadeh
Curated by Papers for Protein Design Using Deep Learning · 4.5 GNN-based · 4.Scaffold to Sequence
January 1, 2026 Chem. Rev. (2026)
De Novo Design of Protein Nanopores: From Minimal Peptides to AI-Driven Design

Anastassia A. Vorobieva, Rituparna Samanta, Toon Van Thillo
Curated by Papers for Protein Design Using Deep Learning · 1. Reviews · 1.1 De novo protein design
January 1, 2026 Advanced Science (2026)
Discriminator-Guided Inverse Folding for Multi-Property Protein Design

Yuchuan Zheng, Chuyi Liu, Zhaoming Liu, Mao Su, Chenyu Tang, Xiang Zheng, Hao Zhang, Jingyuan Li
Curated by Papers for Protein Design Using Deep Learning · 4.5 GNN-based · 4.Scaffold to Sequence
January 1, 2026 Chem. Sci. 2026
HFGuidedDesign: de novo design of cyclic peptide binders via structure-guided discrete diffusion

Haomeng Hu, Renjie Zhu, Ning Zhu, Chengyun Zhang, Tianfeng Shang, Chongyang Li, Jingjing Guo, Xudong Wang, Hongliang Duan
Curated by Papers for Protein Design Using Deep Learning · 5.12 Diffusion-based · 5.Function to Sequence
December 30, 2025 ChemRxiv
Curiosity-driven de novo protein design via polymerized amyloids

Tianyi Jin, Jacob Sass, Wenhao Gao, Connor W. Coley, Alfredo Alexander‐Katz
December 30, 2025 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
Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.2 Diffusion-based
December 29, 2025 arXiv (Cornell University)
End-to-End Test-Time Training for Long Context

Arnuv Tandon, Karan Dalal, Xinhao Li, Daniel Koceja, Marcel Rød, Sam Buchanan, Xiaolong Wang, Jure Leskovec, Sanmi Koyejo, Tatsunori Hashimoto, Carlos Guestrin, Jed McCaleb, Yejin Choi, Yu Sun
December 26, 2025 Journal of Chemical Information and Modeling
Chemprop v2: An Efficient, Modular Machine Learning Package for Chemical Property Prediction

David Graff, Nathan K. Morgan, Jackson W. Burns, Anna C. Doner, Brian Li, Shih‐Cheng Li, Joel Manu, Angiras Menon, Hao‐Wei Pang, Haoyang Wu, Akshat Shirish Zalte, Jonathan Wenyuan Zheng, Connor W. Coley, William H. Green, Kevin P. Greenman
December 24, 2025 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
December 23, 2025 Chemical Science
Structure–activity relationships can be directly extracted from high-throughput crystallographic evaluation of fragment elaborations in crude reaction mixtures

Harold Grosjean, Kate K. Fieseler, Ruben Sanchez-Garcia, Warren Athol Thompson, Charlotte Mary Deane, F. von Delft, Philip Charles Biggin
December 23, 2025 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
Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.3 RoseTTAFold-based
December 23, 2025 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
Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.3 RoseTTAFold-based
December 22, 2025 Quantitative Biology
Protein design and RNA design: Perspectives

Xi Chen, Xu Dai, Peilong Lu
Curated by Papers for Protein Design Using Deep Learning · 1. Reviews · 1.1 De novo protein design
December 22, 2025 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
December 19, 2025 Zenodo (CERN European Organization for Nuclear Research)
LASErMPNN Training Dataset (REDUCE Protonated PDB) [PDB File Format], Chunk 1/2

Benjamin N. Fry, Nicholas F. Polizzi
December 19, 2025 Zenodo (CERN European Organization for Nuclear Research)
LASErMPNN Training Dataset (REDUCE Protonated PDB) [PDB File Format], Chunk 2/2

Benjamin N. Fry, Nicholas F. Polizzi
December 19, 2025 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
Curated by Papers for Protein Design Using Deep Learning · 4.7 Transformer-based · 4.Scaffold to Sequence
December 18, 2025 Journal of Chemical Information and Modeling
Assessing the Chemical Intelligence of Large Language Models

Nicholas T. Runcie, Charlotte Mary Deane, Fergus Imrie
December 18, 2025 bioRxiv (Cold Spring Harbor Laboratory)
FragmentScope - exploring the fragment space with learned surface representations

Evgenia Elizarova, Irina Morozova, Ilia Igashov, Olivia Gampp, David Robin Pavel Iosub, Arne Schneuing, Kelvin Lau, Davide M. Ferraris, Florence Pojer, Roland Riek, Michael M. Bronstein, Bruno E. Correia
December 18, 2025
Author response for "Structure-Activity-Relationships can be directly extracted from high-throughput crystallographic evaluation of fragment elaborations in crude reaction mixtures"

Harold Grosjean, Kate K. Fieseler, Ruben Sanchez-Garcia, Warren Athol Thompson, Charlotte Mary Deane, F. von Delft, Philip Charles Biggin
December 18, 2025
Structural basis for synergistic antibody protection against the essential malaria invasion complex protein RIPR

Barnabas G. Williams, Jordan R. Barrett, Josefin Bartholdson Scott, Cassandra A. Rigby, Matteo Cagiada, Doris Quinkert, Kirsty McHugh, Anna Gesine Huhn, Sean Anthony Burnap, Camille Gourjault, Francesca Byrne, Sai Sundar Rajan Raghavan, Ana Rodrigues, Laura Bergamaschi, Beatrice Balzarotti, Simon J. Watson, Noah Miller, Lloyd D. W. King, Francesca R. Donnellan, Camilla A. Gladstone, Jemima Paterson, Stefania Scalabrino, Sarah E. Silk, Jo Salkeld, Angela M. Minassian, Katherine Skinner, Weston B. Struwe, Charlotte Mary Deane, Stephen T. Reece, Andrew B. Ward, Simon J. Draper
December 16, 2025 bioRxiv (Cold Spring Harbor Laboratory)
De novo design of protein competitors for small molecule immunosensing

Yosta de Stigter, Tallie Godschalk, Maarten Merkx
Curated by Papers for Protein Design Using Deep Learning · 2. Model-based design · 2.1.1 trRosetta-based
December 15, 2025 arXiv (Cornell University)
Olmo 3

Team OLMo, Allyson Ettinger, Amanda Bertsch, Bailey Kuehl, Graham, David, David Heineman, Dirk Groeneveld, Faeze Brahman, Finbarr Timbers, Hamish Ivison, Jacob Morrison, Jake Poznanski, Kyle Lo, Luca Soldaini, Matt Jordan, Mayee F. Chen, Michael Noukhovitch, Nathan Lambert, Walsh, Pete, Pradeep Dasigi, Robert Berry, Saumya Malik, Saurabh Anil Shah, Scott Geng, Shane Arora, Shashank Rai Gupta, Anderson, Taira, Xiao, Teng, Murray, Tyler, Tyler Romero, Victoria Graf, Akari Asai, Akshita Bhagia, Alexander Wettig, Alisa Liu, Aman Rangapur, Chloe Anastasiades, Huang, Costa, Dustin Schwenk, Harsh K. Trivedi, Ian Magnusson, Jaron Lochner, Jiacheng Liu, Lester James V. Miranda, Maarten Sap, Morgan, Malia, Schmitz, Michael, Michal Guerquin, Wilson, Michael, Regan Huff, Ronan Joseph Le Bras, Rui Xin, Rulin Shao, Sam Skjonsberg, Shannon Zejiang Shen, Shuyue Stella Li, Tucker Wilde, Valentina Pyatkin, Merrill, Will, Chang, Yapei, Yuling Gu, Zhiyuan Zeng, Ashish Sabharwal, Luke Zettlemoyer, Pang Wei Koh, Farhadi, Ali, Noah A. Smith, Hannaneh Hajishirzi
December 14, 2025 IEEE International Workshop on Computational Advances in Multi-Sensor Adaptive Processing
On the Impact of Downstream Tasks on Sampling and Reconstructing Noisy Graph Signals

Baskaran Sripathmanathan, Xiaowen Dong, Michael M. Bronstein
December 13, 2025 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
Curated by Papers for Protein Design Using Deep Learning · 2. Model-based design · 2.1.1 trRosetta-based
December 10, 2025 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
Curated by Papers for Protein Design Using Deep Learning · 5.4 Transformer-based · 5.Function to Sequence
December 9, 2025 bioRxiv (Cold Spring Harbor Laboratory)
Protein Diffusion Models as Statistical Potentials

James P. Roney, Chenxi Ou, Sergey Ovchinnikov
December 9, 2025
Author response: Evidence of social learning across symbolic cultural barriers in sperm whales

Antonio Leitao, Maxime Lucas, Simone Poetto, Taylor A. Hersh, Shane Gero, David F. Gruber, Michael M. Bronstein, Giovanni Petri
December 5, 2025 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
December 5, 2025 Advanced Engineering Informatics
Learning constrained static equilibrium for thrust network inverse form-finding via physics-informed geometric deep learning on CW complexes

Kam-Ming Mark Tam, Nathan Collin Brown, Michael M. Bronstein, Tom Van Mele, Philippe Block
December 5, 2025 arXiv (Cornell University)
Mechanistic Interpretability of Antibody Language Models Using SAEs

Haque, Rebonto, Oliver M. Turnbull, Anisha Parsan, Nithin Parsan, John Jeongseok Yang, Anna L. Beukenhorst, Charlotte Mary Deane
December 4, 2025 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
December 3, 2025 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
December 3, 2025 bioRxiv (Cold Spring Harbor Laboratory)
A foundation model for microbial growth dynamics

Zachary A. Holmes, Irida Shyti, Alexandra L. Hoffman, Katherine E. Duncker, Helena R. Ma, Zhengqing Zhou, Dongheon Lee, Rohan Maddamsetti, Kyeri Kim, Emrah Şimşek, Grayson S. Hamrick, Hye-In Son, César A. Villalobos, Jia Grace Lu, Yuanchi Ha, Ashwini R. Shende, Zhixiang Yao, Sizhe Liu, Daniel Mark Shapiro, Kseniia Kholina, Harris M. Davis, Yasa Baig, Feilun Wu, Shangying Wang, Xiran Wang, Pranam Chatterjee, Michael Lynch, Allison J. Lopatkin, Lawrence A. David, Emma J. Chory, Lingchong You
December 2, 2025 International Journal of Molecular Sciences
Development of Plasma Protein Classification Models for Alzheimer’s Disease Using Multiple Machine Learning Approaches

Amy Tsurumi, Catherine M. Cahill, Andy Liu, Pranam Chatterjee, Sudeshna Das, Ami Kobayashi
December 2, 2025 Expert Opinion on Drug Discovery
From algorithms to systems: integrating computation into drug discovery

Anthony R Bradley, Adrian Rossall, Garry Pairaudeau, Charlotte Mary Deane
December 2, 2025 Cell
The unique architecture of umbrella toxins permits a two-tiered molecular bet-hedging strategy for interbacterial antagonism

Qinqin Zhao, J. Vlach, Young‐Jun Park, Yongjun Tan, Savannah K Bertolli, Pooja Srinivas, Pinyu Liao, Connor R. Fitzpatrick, Jeffery L. Dangl, Parastoo Azadi, Frank DiMaio, Snow Brook Peterson, Dapeng Zhang, David Veesler, Joseph D. Mougous
December 2, 2025 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
December 2, 2025 arXiv (Cornell University)
Self-Improving VLM Judges Without Human Annotations

Inna Wanyin Lin, Yushi Hu, Shuyue Stella Li, Scott Geng, Pang Wei Koh, Luke Zettlemoyer, Tim Althoff, Marjan Ghazvininejad
December 2, 2025 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
Curated by Papers for Protein Design Using Deep Learning · 5.7 Flow-based · 5.Function to Sequence
December 1, 2025 npj Women s Health
Identifying nutraceutical targets to treat polycystic ovary syndrome using graph representation learning

Simon Hanassab, Joshua Southern, Ayomide Victoria Olabode, Ivan Laponogov, Michael M. Bronstein, Alexander N. Comninos, Thomas Heinis, Ali Abbara, Chioma N. Izzi‐Engbeaya, Kirill Veselkov, Waljit Singh Dhillo
December 1, 2025 Cell Reports Medicine
Lymphodepleting chemotherapy potentiates neoantigen-directed T cell therapy by enhancing antigen presentation

Shira Sagie, Tomer Babu, Chen Weller, Claire Tabachnik, Ido Livneh, Nele P. Quast, Nofar Gumpert, Alina S. Shomuradova, Matthew I. J. Raybould, Ronen Levy, Dmitry B. Malko, Adi Alfia, Talal Ben Lulu, Michal Alon, Franco Herrera, Mikhail A. Kutuzov, Mirie Zerbib, Polina Greenberg, Talya Wasserman-Bartov, Gil Benedek, Yishai Levin, Chani Stossel, Iris Kamer, Talia Golan, Roni Oren, Merav D. Shmueli, Osnat Bartok, Jair Bar, Jonathan E. Cohen, Omer Dushek, Charlotte Mary Deane, Yardena Samuels
November 29, 2025 arXiv (Cornell University)
Efficient and Programmable Exploration of Synthesizable Chemical Space

Shitong Luo, Connor W. Coley
November 27, 2025 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
Curated by Papers for Protein Design Using Deep Learning · 5.4 Transformer-based · 5.Function to Sequence
November 26, 2025 bioRxiv (Cold Spring Harbor Laboratory)
PULSAR: a Foundation Model for Multi-scale and Multicellular Biology

Kuan Pang, Yanay Rosen, Kasia Kedzierska, Ziyuan He, Abhejit Rajagopal, Claire E. Gustafson, Grace H. Huynh, Jure Leskovec
November 24, 2025 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
November 24, 2025 arXiv (Cornell University)
Flow Map Distillation Without Data

Tong, Shangyuan, Ma, Nanye, Xie, Saining, Tommi Jaakkola
November 24, 2025 arXiv (Cornell University)
DR Tulu: Reinforcement Learning with Evolving Rubrics for Deep Research

Shao, Rulin, Asai, Akari, Shen, Shannon Zejiang, Ivison, Hamish, Kishore, Varsha, Zhuo, Jingming, Xinran Zhao, Park, Molly, Samuel G. Finlayson, David Alexander Sontag, Murray, Tyler, Min, Sewon, Dasigi, Pradeep, Soldaini, Luca, Brahman, Faeze, Yih, Wen-tau, Tongshuang Wu, Luke Zettlemoyer, Kim, Yoon, Hajishirzi, Hannaneh, Pang Wei Koh
November 24, 2025 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
Curated by Papers for Protein Design Using Deep Learning · 5.4 Transformer-based · 5.Function to Sequence
November 24, 2025 bioRxiv (Cold Spring Harbor Laboratory)
General-Purpose Large Language Models, such as DeepSeek V3.2, Have Evolved Protein Design Capabilities

Jiawei Li, Xinxiu Dong
Curated by Papers for Protein Design Using Deep Learning · 5.4 Transformer-based · 5.Function to Sequence
November 24, 2025 arXiv (Cornell University)
Torsion-Space Diffusion for Protein Backbone Generation with Geometric Refinement

Singh, Lakshaditya, Shelke, Adwait, Agrawal, Divyansh
Curated by Papers for Protein Design Using Deep Learning · 3. Function to Scaffold · 3.4 Diffusion-based
November 22, 2025 Nucleic Acids Research
Structure-informed models for ionic current prediction in nanopore sequencing of expanded dna alphabets

Ashley P. Stephenson, Jayson Sumabat, Hinako Kawabe, Sidharth Lakshmanan, Hyo Joong Kim, Yubing Li, Jorge A. Marchand, Jeff Nivala
November 20, 2025 bioRxiv (Cold Spring Harbor Laboratory)
Generating Hybrid Proteins with the MSA-Transformer

Sanjana Tule, Samuel Davis, Ivan Koludarov, Ariane Mora, Mikael Bodén A
November 20, 2025 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
November 20, 2025 arXiv (Cornell University)
CONFIDE: Hallucination Assessment for Reliable Biomolecular Structure Prediction and Design

Zijun Gao, Mutian He, Sun, Shijia, Hanqun Cao, Jingjie Zhang, Zihao Luo, Xiaorui Wang, Yao, Xiaojun, Chang‐Yu Hsieh, Chunbin Gu, Pheng‐Ann Heng
Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.9 AlphaFold-based
November 19, 2025 Nature
Semantic design of functional de novo genes from a genomic language model

Aditi T. Merchant, Samuel H. King, Eric Nguyen, Brian Hie
November 19, 2025 Zenodo (CERN European Organization for Nuclear Research)
sokrypton/af2bind: final version for publication

Artem G, Sergey Ovchinnikov
November 18, 2025 bioRxiv (Cold Spring Harbor Laboratory)
CIRPIN: Learning Circular Permutation-Invariant Representations to Uncover Putative Protein Homologs

Aiden R. Kolodziej, S. Mazdak Abulnaga, Sergey Ovchinnikov
November 17, 2025 bioRxiv (Cold Spring Harbor Laboratory)
Hit or Miss: Understanding Emergence and Absence of Homo-oligomeric Contacts in Protein Language Models

Zhidian Zhang, Yo Akiyama, Yehlin Cho, Samarth Jajoo, Sergey Ovchinnikov
November 14, 2025 medRxiv
Editing stem cell genomes at scale to measure variant effects in diverse cell and genetic contexts

Shawn Fayer, Riddhiman K. Garge, Melissa Hopkins, Clayton E. Friedman, Abby V. McGee, Joshua Rico, Rachel L. Powell, Evan McDermot, Nahum T. Smith, Sriram Pendyala, Marcy E. Richardson, Erica D. Smith, B. Monica Bowen, Rebecca Resnick, Pankhuri Gupta, Andrew B. Stergachis, Casey A. Gifford, Sudarshan Pinglay, Kai‐Chun Yang, Douglas M. Fowler, Lea M. Starita
November 13, 2025 bioRxiv (Cold Spring Harbor Laboratory)
Transferable Transcriptional Topic Modeling Traces Medulloblastoma Subtypes to Distinct Cerebellar Developmental States

Ashmitha Rajendran, Parthiv Haldipur, Sonali Arora, Kaustubh Grama, Saanvi S. Subramanian, Leyre Merino Galan, David Johnson, Kimberly A. Aldinger, Jay Shendure, Kathleen J. Millen, John H. Gennari, Siobhan S. Pattwell
November 13, 2025 EMPIAR dataset
GDH in complex with compound G2, processed with cryoPARES

Rubén Sánchez-García, Berndt A, Apelbaum A, Reeks J, Williams PA, Carl R. Poelking, Charlotte Mary Deane, Michael Saur
November 13, 2025 bioRxiv (Cold Spring Harbor Laboratory)
Harnessing protein-folding algorithms to drug intrinsically disordered epitopes

Jakub Lála, Stefano Angioletti‐Uberti
Curated by Papers for Protein Design Using Deep Learning · 2. Model-based design · 2.4 LLM-based
November 12, 2025 bioRxiv (Cold Spring Harbor Laboratory)
Uncovering the flexibility of CDR loops in antibodies and TCRs through large-scale molecular dynamics

Matteo Cagiada, Fabian C. Spoendlin, King Ifashe, Charlotte Mary Deane
November 12, 2025 arXiv (Cornell University)
Controllable protein design with particle-based Feynman-Kac steering

Erik Hartman, Jonas Wallin, Johan A. Malmström, Jimmy Olsson
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
November 11, 2025 Nature Biotechnology
A parts list of promoters and gRNA scaffolds for mammalian genome engineering and molecular recording

Troy A. McDiarmid, Megan L. Taylor, Wei Chen, Florence M. Chardon, Junhong Choi, Hanna Liao, Xiaoyi Li, Haedong Kim, Jean‐Benoît Lalanne, Tony Yi‐Wei Li, Jenny F. Nathans, Beth Martin, Jordan Knuth, Alessandro Luis Venega Coradini, Jesse M. Gray, Sudarshan Pinglay, Jay Shendure
November 10, 2025 ACS Nano
Random Heteropolymers Enable Nonspecific Protein Binding and Loop-Mediated Stabilization

Tianyi Jin, Akorfa Dagadu, Connor W. Coley, Alfredo Alexander‐Katz
November 10, 2025 Communications Chemistry
Inferring residue level hydrogen deuterium exchange with ReX

Oliver M. Crook, Nathan Gittens, Chun‐wa Chung, Charlotte Mary Deane
November 10, 2025 arXiv (Cornell University)
RLVE: Scaling Up Reinforcement Learning for Language Models with Adaptive Verifiable Environments

Zhiyuan Zeng, Hamish Ivison, Wang, Yiping, Lifan Yuan, Shuyue Stella Li, Zhuorui Ye, Siting Li, Jacqueline He, Runlong Zhou, Tong Chen, Chenyang Zhao, Yulia Tsvetkov, Simon S. Du, Natasha Jaques, Hao Peng, Pang Wei Koh, Hannaneh Hajishirzi
November 10, 2025 Stanford Digital Repository
Automating discovery with AI

Kexin Huang, Jure Leskovec, Emmanuel J. Candès, Anshul Bharat Kundaje, Stanford University. School of Engineering., Stanford University. Computer Science Department.
November 10, 2025 PubMed
Entangled Schrödinger Bridge Matching

Tang, Sophia, Zhang, Yinuo, Pranam Chatterjee
November 9, 2025 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
Curated by Papers for Protein Design Using Deep Learning · 2. Model-based design · 2.1.1 trRosetta-based
November 8, 2025 arXiv (Cornell University)
Joint Design of Protein Surface and Structure Using a Diffusion Bridge Model

Li, Guanlue, Xufeng Zhao, Fang Wu, Laue, Sören
Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.2 Diffusion-based
November 7, 2025 arXiv (Cornell University)
Peptide2Mol: A Diffusion Model for Generating Small Molecules as Peptide Mimics for Targeted Protein Binding

He, Xinheng, Zhang, Yijia, Lin, Haowei, Peng, Xingang, Kong, Xiangzhe, Li, Mingyu, Ma, Jianzhu
Curated by Papers for Protein Design Using Deep Learning · 6. Function to Structure · 6.2 Diffusion-based
November 5, 2025 bioRxiv (Cold Spring Harbor Laboratory)
Large-scale discovery of neural enhancers for cis-regulation therapies

Troy A. McDiarmid, Nicholas F. Page, Florence M. Chardon, Riza M. Daza, George T Chen, Michael Kosicki, Lucas M. James, Hannah C. Nourie, Dianne Laboy Cintrón, Arthur S. Lee, Paula A Vij, Diego Calderon, Jean‐Benoît Lalanne, Beth Martin, Kyle D. Fink, Michael E. Talkowski, Alysson Renato Muotri, Benjamin D. Philpot, Len A. Pennacchio, Daniel H. Geschwind, Stephan Sanders, Nadav Ahituv, Jay Shendure
November 5, 2025 bioRxiv (Cold Spring Harbor Laboratory)
Adaptive resampling for improved machine learning in imbalanced single-cell datasets

Zeinab Navidi, Akshaya Thoutam, Madeline Hughes, Srivatsan Raghavan, Peter S. Winter, Lorin A. Crawford, Ava P. Amini
November 5, 2025 EMPIAR dataset
GDH in complex with ADP, processed with cryoPARES

Rubén Sánchez-García, Berndt A, Apelbaum A, Reeks J, Williams PA, Carl R. Poelking, Charlotte Mary Deane, Michael Saur
November 5, 2025 EMPIAR dataset
GDH in complex with compound G1, processed with cryoPARES

Rubén Sánchez-García, Berndt A, Apelbaum A, Reeks J, Williams PA, Carl R. Poelking, Charlotte Mary Deane, Michael Saur
November 4, 2025 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
November 4, 2025 arXiv (Cornell University)
A Roadmap for Predictive Human Immunology

Khan, Aly A., Perera, Jason, James Zou, Löıc A. Royer, Alan R. Lowe, Carr, Ambrose, Karaletsos, Theofanis, Brennan, Patricia, Parsa, Roham, Clark, Marcus R., Joseph L. DeRisi, Jay Shendure, Schmid, Sandra L., Fraser, Scott E., Califano, Andrea, Kelley, Shana O.
November 3, 2025 Proceedings of the National Academy of Sciences
Conformational regulation of two essential activators of bacterial cell elongation

Morgan S. A. Gilman, Irina Shlosman, Daniel D. Samé Guerra, Masy Domecillo, Elayne M. Fivenson, Claire Bourett, Thomas G. Bernhardt, Nicholas F. Polizzi, Joseph J. Loparo, Andrew C. Kruse
November 3, 2025 arXiv (Cornell University)
Identification of Capture Phases in Nanopore Protein Sequencing Data Using a Deep Learning Model

Martin, Annabelle, Daphne Kontogiorgos-Heintz, Jeff Nivala
November 3, 2025 Blood
Interim Results of the CMML scrna-seq atlas: GMP skewing is independently associated with overall survival in CMML.

Amy F. McLemore, Surendra Neupane, Zena Komrokji, Maria E. Balasis, Traci L. Kruer, Umesh Padia, Sean Murphy, Aline Renneville, Nathalie M Droin, Dorothée Selimoglu‐Buet, Miguel Ángel González Martínez, Chaomei H. Zhang, Tania Mesa, Sean Yoder, David Andrew Sallman, Andrew Tucker Kuykendall, Christopher B. Ryder, Rami S. Komrokji, Mrinal M. Patnaik, Meghan C. Ferrall‐Fairbanks, Regina Barzilay, Éric Solary, Eric Padron
November 3, 2025 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.
Curated by Papers for Protein Design Using Deep Learning · 1. Reviews · 1.1 De novo protein design
November 2, 2025 ACS Chemical Biology
Orthogonal IMiD-Degron Pairs Induce Selective Protein Degradation in Cells

Patrick J. Brennan, Rebecca E. Saunders, Mary Spanou, Sarah E. Singleton, M. Teresa Serafini, Liang Sun, Guillaume Heger, Agnieszka Konopacka, Ryan D. D. Beveridge, C. Cameron Taylor, Peter DePaola, Laurie Gordon, Shenaz B. Bunally, Aurore Saudemont, Andrew B. Benowitz, Carlos Martinez-Fleites, Danielle L. Schmitt, Robert D. Damoiseaux, Markus A. Queisser, Heeseon An, Charlotte Mary Deane, Michael M. Hann, Lewis L. Brayshaw, Stuart J. Conway
November 2, 2025 arXiv (Cornell University)
HarnessLLM: Automatic Testing Harness Generation via Reinforcement Learning

Yujian Liu, Jiabao Ji, Yang Zhang, Wenbo Guo, Tommi Jaakkola, Shiyu Chang
November 2, 2025 Infoscience (Ecole Polytechnique Fédérale de Lausanne)
Bridging Graph Neural Networks and Large Language Models: A Survey and Unified Perspective

Álvaro Arroyo, Federico Barbero, Hugh Blayney, Michael M. Bronstein, Xiaowen Dong, Pietro Liò, Razvan Pascanu, Pierre Vandergheynst
November 1, 2025 bioRxiv (Cold Spring Harbor Laboratory)
Single-cell, multi-region profiling of the macaque brain across the lifespan

Wei Yang, Kirsty Watkins, Alex R. DeCasien, Mary B. O’Neill, Martin O. Bohlen, Diana R. O’Day, Madeleine Duran, Chengxiang Qiu, A. N. Meleshko, Anh Vo, Melia Menke, Diego Calderon, Jérôme Sallet, James P. Higham, Melween I. Martínez, Cole Trapnell, Lea M. Starita, Michael J. Montague, Michael L. Platt, Kenneth L. Chiou, Jay Shendure, Noah Snyder‐Mackler
October 28, 2025 arXiv (Cornell University)
LeMat-Synth: a multi-modal toolbox to curate broad synthesis procedure databases from scientific literature

Magdalena Lederbauer, Siddharth Betala, Valerie Gentzke, Anamaria Leonescu, Amine Sehaba, Faris Flaifil, Ayush Jain, Alfonso Amayuelas, Nikhil Yelamarthy, Li, Xiyao, Germain, Grégoire, Stefano Ribes, Stefan P. Schmid, Alexandre Nozadze, Anna Kelmanson, Sudheesh Kumar Ethirajan, Mohd Zaki, Elton Pan, Georgia Channing, Connor W. Coley, Philippe Schwaller, Rocío Mercado, Alexandre Duval, Mathilde L. D. Franckel, S. Gleason
October 24, 2025 Nature Biotechnology
Democratizing protein language model training, sharing and collaboration

Jin Su, Zhikai Li, Tianli Tao, Chenchen Han, Yan He, Fengyuan Dai, Qingyan Yuan, Yuan Gao, Tong Si, Xuting Zhang, Yuyang Zhou, Junjie Shan, Xibin Zhou, Xing Chang, Shiyu Jiang, Dacheng Ma, The OPMC, Anthony Gitter, Milot Mirdita, Kevin Yang, Pascal Notin, Debora S. Marks, Pranam Chatterjee, Rohit Singh, Philip A. Romero, Michael Heinzinger, Jianming Liu, Jia Zheng, Stan Ziqing Li, An‐Ping Zeng, Huaizong Shen, Jijie Chai, Feng Ju, Noelia Ferruz, Anum Azam Glasgow, Philip M. Kim, Christopher Davis Snow, Vasilis Ntranos, Jianyi Yang, Liang Hong, Caixia Gao, Tong Si, Michael M. Bronstein, Xing Chang, Fajie Yuan, Jin Su, Zhikai Li, Tianli Tao, Chenchen Han, Yan He, Fengyuan Dai, Xuting Zhang, Yuyang Zhou, Junjie Shan, Xibin Zhou, Shiyu Jiang, Yuan Gao, Jiawei Zhang, Yuliang Fan, Yuyang Tao, Linqi Cheng, Xinzhe Zheng, Lei Chen, Rui Long, Lingjie Kong, Zhongji Pu, Jiaming Guan, Tianyuan Zhang, Cheng Li, Martin Steinegger, Sergey Ovchinnikov, Fajie Yuan
Curated by Papers for Protein Design Using Deep Learning · 4.7 Transformer-based · 4.Scaffold to Sequence
October 24, 2025 Journal of Molecular Biology
HeavyBuilder: Analysis of High-Throughput of Antibody Heavy Chain Repertoires in the Structural Space

João Henrique Diniz Brandão Gervásio, Alexander Greenshields‐Watson, Nele P. Quast, Brennan Abanades, Liza Figueiredo Felicori, Charlotte Mary Deane
October 24, 2025 Nature Microbiology
Author Correction: Discovery and artificial intelligence-guided mechanistic elucidation of a narrow-spectrum antibiotic

Denise B. Catacutan, Vian Tran, Autumn Arnold, Jeremie Alexander, Gabriele Corso, Yeganeh Yousefi, Megan M. Tu, Stewart McLellan, Dominique Tertigas, Kimberly Corneil, Jakob Magolan, Michael Gordon Surette, Eric D. Brown, Brian K. Coombes, Regina Barzilay, Jonathan M. Stokes
October 24, 2025 arXiv (Cornell University)
Generalised Flow Maps for Few-Step Generative Modelling on Riemannian Manifolds

Oscar Davis, Michael S. Albergo, Nicholas M. Boffi, Michael M. Bronstein, Avishek Joey Bose
October 21, 2025 ACS Nano
AI-Guided Hydrophobic Core Design of Robust Six-Helix Bundle Proteins

Yinying Meng, Guojin Tang, Ruishi Wang, Bin Zheng, Yuanhao Liu, Hantian Zhang, Peng Zheng
Curated by Papers for Protein Design Using Deep Learning · 4.5 GNN-based · 4.Scaffold to Sequence