Accurate structure prediction of biomolecular interactions with AlphaFold 3
Josh Abramson, Jonas Adler, John M. Jumper · Large collaboration of ~47 authors from Google DeepMind and Isomorphic Labs; corresponding authors include John Jumper and Demis Hassabis. Other authors include Jack Dunger, Richard Evans, Tim Green. Note: input gave 'AlphaFold3'; the published title uses 'AlphaFold 3' (with a space).
Summary
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.
Key findings
- A single diffusion-based architecture predicts structures across protein, nucleic acid, ligand, ion, and modified-residue complexes within one framework.
- AlphaFold 3 outperformed leading docking and prediction tools on protein-ligand, protein-nucleic acid, and antibody-antigen interactions.
- The model demonstrated broad generalization across biomolecular interaction types, advancing modeling of cellular machinery.
Subjects & keywords
Cite this paper
Josh Abramson, Jonas Adler, & John M. Jumper [Large collaboration of ~47 authors from Google DeepMind and Isomorphic Labs; corresponding authors include John Jumper and Demis Hassabis. Other authors include Jack Dunger, Richard Evans, Tim Green. Note: input gave 'AlphaFold3'; the published title uses 'AlphaFold 3' (with a space).] (2024). Accurate structure prediction of biomolecular interactions with AlphaFold 3. Nature. https://doi.org/10.1038/s41586-024-07487-w
@article{abramson2024accurate,
author = {Josh Abramson and Jonas Adler and John M. Jumper and {Large collaboration of ~47 authors from Google DeepMind and Isomorphic Labs; corresponding authors include John Jumper and Demis Hassabis. Other authors include Jack Dunger, Richard Evans, Tim Green. Note: input gave 'AlphaFold3'; the published title uses 'AlphaFold 3' (with a space).}},
title = {Accurate structure prediction of biomolecular interactions with AlphaFold 3},
journal = {Nature},
year = {2024},
doi = {10.1038/s41586-024-07487-w},
url = {https://doi.org/10.1038/s41586-024-07487-w}
}