Atomic functional site scaffolding in biopolymers with RFdiffusion3
The catalytic and other sophisticated functions of biomolecules arise from the placement of many atoms in three-dimensional space. Here, we describe a generative artificial intelligence method for biopolymers, RFdiffusion3 (RFD3), which employs free atom diffusion to satisfy complex sets of atomic constraints more rapidly and accurately than previous methods across several challenges from enzyme design to RNA structure design. We demonstrate experimentally the power of the RFD3 pipeline for enzyme design by designing de novo phosphotriesterases with a complex active site architecture incorporating a carbamylated lysine coordinating two metal ions and zinc proteases specific for the transthyretin protein involved in amyloid diseases; in both cases we obtain active catalysts in zero shot 96 construct design campaigns.
Authors
- Brian Coventry (ORCID: https://orcid.org/0000-0002-6910-6255)
- Yuliya Politanska (ORCID: https://orcid.org/0000-0002-6766-988X)
- Jonathan Funk (ORCID: https://orcid.org/0009-0006-9496-1890)
- Raktim Mitra (ORCID: https://orcid.org/0000-0003-1182-3742)
- An‐Qi Chen (ORCID: https://orcid.org/0000-0001-9857-0594)
- Rohith Krishna (ORCID: https://orcid.org/0009-0003-6387-9622)
- Helen E. Eisenach (ORCID: https://orcid.org/0000-0002-3201-4517)
- Simon V. Mathis (ORCID: https://orcid.org/0000-0002-5246-6481)
- Kieran Didi (ORCID: https://orcid.org/0000-0001-6839-3320)
- Jie Chen (ORCID: https://orcid.org/0000-0001-9609-669X)
- David A. Baker (ORCID: https://orcid.org/0000-0001-7896-6217)
- Andrew Favor (ORCID: https://orcid.org/0000-0002-9977-2785)
- Paul T. Kim (ORCID: https://orcid.org/0000-0002-8950-7179)
- Rafael I. Brent (ORCID: https://orcid.org/0000-0002-3233-7914)
- Florence J. Hardy (ORCID: https://orcid.org/0000-0003-0671-0209)
- Seth M. Woodbury (ORCID: https://orcid.org/0000-0003-0510-8240)
- Enisha Sehgal (ORCID: https://orcid.org/0000-0002-6000-0999)
- Lars L. Schaaf (ORCID: https://orcid.org/0000-0002-1935-236X)
- Andrew Kubaney (ORCID: https://orcid.org/0009-0009-4982-6050)
- Kejia Wu (ORCID: https://orcid.org/0000-0002-4532-4290)
- Frank DiMaio (ORCID: https://orcid.org/0000-0002-7524-8938)
- Bo Qiang (ORCID: https://orcid.org/0000-0001-7428-4104)
- Odin Zhang (ORCID: https://orcid.org/0000-0002-6734-1534)
- Nathaniel Corley (ORCID: https://orcid.org/0000-0002-6509-7144)
- Saman Salike (ORCID: https://orcid.org/0009-0007-1060-0287)
- Antonia Ruder (ORCID: https://orcid.org/0009-0006-4962-9573)
- Maxwell W. Kazman (ORCID: https://orcid.org/0000-0003-4420-4016)
- Aiko Muraishi (ORCID: https://orcid.org/0009-0000-1212-2695)
- Yanjing Li
- Jasper Butcher (ORCID: https://orcid.org/0009-0004-4864-1330)
- Donghyo Kim
- Tuscan Rock Thompson (ORCID: https://orcid.org/0009-0003-1876-106X)
- Gabriela Bastidas Reinoso (ORCID: https://orcid.org/0009-0006-1199-564X)
Institutions
- Howard Hughes Medical Institute (US)
- University of Washington (US)
- University of Cambridge (GB)
- Novo Nordisk Foundation (DK)
- ETH Zurich (CH)
- University of Oxford (GB)
- Nvidia (United States) (US)
- Technical University of Denmark (DK)
Publication Details
- Journal
- Science
- Published
- 2026-10-15
- DOI
- https://doi.org/10.1126/science.aeh2982
- Primary Topic
- Protein Structure and Dynamics
- Type
- article
- Field-Weighted Citation Impact
- 0.00