diffusion model — papers

BiologyNature · May 2024 Open access

Accurate structure prediction of biomolecular interactions with AlphaFold 3

Josh Abramson, Jonas Adler and John M. Jumper

This paper introduced AlphaFold 3, a unified deep learning model that predicts the joint structure of complexes containing proteins, nucleic acids, small-molecule ligands, ions, and modified residues. It replaces much of the prior architecture with a diffusion-based module that directly generates atomic coordinates. The model achieved substantially improved accuracy over specialized tools across many interaction types, including protein-ligand and protein-nucleic acid complexes.

alphafold3 biomolecular interactions diffusion model protein-ligand

BiologyNature · Jul 2023 Open access

De novo design of protein structure and function with RFdiffusion

Joseph L. Watson, David Juergens and David Baker

This paper introduced RFdiffusion, a generative diffusion model built on the RoseTTAFold network for de novo protein design. It enables a range of design tasks, including unconditional generation, symmetric oligomer design, functional motif scaffolding, and binder design. Many designs were experimentally validated, with solved structures closely matching the intended models.

protein design de novo design diffusion model rfdiffusion