Science (New York, N.Y.) · 2026
Atomic functional site scaffolding in biopolymers with RFdiffusion3.
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Butcher Jasper, Krishna Rohith, Mitra Raktim, Woodbury Seth M, Kim Donghyo, Brent Rafael I, Li Yanjing, Corley Nathaniel, Favor Andrew, Chen Anqi, Kim Paul T, Funk Jonathan, Reinoso Gabriela Bastidas, Wu Kejia, Muraishi Aiko, Eisenach Helen E, Salike Saman, Mathis Simon, Thompson Tuscan Rock, Ruder Antonia, Sehgal Enisha, Kubaney Andrew, Chen Jie, Politanska Yuliya, Coventry Brian, Zhang Odin, Hardy Florence J, Qiang Bo, Didi Kieran, Kazman Maxwell, Schaaf Lars L, DiMaio Frank, Baker David
Аннотация
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.