<i>De novo</i> Design of All-atom Biomolecular Interactions with RFdiffusion3.

ABSTRACT: Deep learning has accelerated protein design, but most existing methods are restricted to generating protein backbone coordinates and often neglect interactions with other biomolecules. We present RFdiffusion3 (RFD3), a diffusion model that generates protein structures in the context of ligands, nucleic acids and other non-protein constellations of atoms. Because all polymer atoms are modeled explicitly, conditioning the model on complex sets of atom-level constraints for enzyme design and other challenges is both simpler and more effective than previous approaches. RFD3 achieves improved performance compared to prior approaches on a range of in silico benchmarks with one tenth the computational cost. Finally, we demonstrate the broad applicability of RFD3 by designing and experimen

SUBMITTER: Butcher J 

PROVIDER: S-EPMC12458353 | biostudies-literature | 2025 Nov

REPOSITORIES: biostudies-literature