Accurate structure prediction of biomolecular interactions with AlphaFold 3

2024/05/08 by Josh Abramson, Jonas Adler, Jack Dunger +45 · 1 voice · 665 citations
Biochemistry, Genetics and Molecular Biology · #Protein Structure and Dynamics

paper · pdf · doi:10.1038/s41586-024-07487-w

openalex publication_date 2024/05/08 · openalex created_date 2025/10/10 · openalex updated_date 2026/07/31

Abstract

Abstract The introduction of AlphaFold 2 1 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 . Here we describe our AlphaFold 3 model with a substantially updated diffusion-based architecture that is capable of predicting the joint structure of complexes including proteins, nucleic acids, small molecules, ions and modified residues. The new AlphaFold model demonstrates substantially improved accuracy over many previous specialized tools: far greater accuracy for protein–ligand interactions compared with state-of-the-art docking tools, much higher accuracy for protein–nucleic acid interactions compared with nucleic-acid-specific predictors and substantially higher antibody–antigen prediction accuracy compared with AlphaFold-Multimer v.2.3 7,8 . Together, these results show that high-accuracy modelling across biomolecular space is possible within a single unified deep-learning framework.

Citations

• AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading
• Highly accurate protein structure prediction with AlphaFold
• Accurate prediction of protein structures and interactions using a three-track neural network
• State-specific protein-ligand complex structure prediction with a multi-scale deep generative model
• DiffDock: Diffusion Steps, Twists, and Turns for Molecular Docking
• Survey of Hallucination in Natural Language Generation
• Evolutionary-scale prediction of atomic-level protein structure with a language model
• Generalized Biomolecular Modeling and Design with RoseTTAFold All-Atom
• Scoring function for automated assessment of protein structure template quality

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• Accurate structure prediction of biomolecular interactions with AlphaFold 3 doi.org/10.1038/s415... But: no code, no binary, and what appears to be a limited webserver [bsky, 3 points, 2 comments]

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