Accurate structure prediction of biomolecular interactions with AlphaFold 3

Abstract

The introduction of AlphaFold 2¹ has spurred a revolution in modelling the structure of proteins and their interactions, enabling a huge range of applications in protein modelling and design^2-6. In this paper, we describe our AlphaFold 3 model with a substantially updated diffusion-based architecture, which is capable of joint structure prediction of complexes including proteins, nucleic acids, small molecules, ions, and modified residues. The new AlphaFold model demonstrates significantly improved accuracy over many previous specialised tools: far greater accuracy on protein-ligand interactions than state of the art docking tools, much higher accuracy on protein-nucleic acid interactions than nucleic-acid-specific predictors, and significantly higher antibody-antigen prediction accuracy than AlphaFold-Multimer v2.3^7,8. Together these results show that high accuracy modelling across biomolecular space is possible within a single unified deep learning framework.