· 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
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Abstract
This zip file contains the following structures as mmcifs for all designs in Wu et al. 2026, "De novo enzyme design for new-to-nature chemistry with AlphaProtein Novo". *_apn: the sampled structure from the AP Novo diffusion model. *_lmpnn: where applicable, the LigandMPNN-redesigned structure. Sidechains are removed from non-motif residues as they have changed amino-acid type. *_af3: AF3-predicted structure of the design in complex with the ligand(s) that are present in the input motif for diffusion generation.