Accurate structure prediction of biomolecular interactions with AlphaFold 3

Josh Abramson, Jonas Adler, Jack Dunger, Richard Evans, Tim Green, Alexander Pritzel, Olaf Ronneberger, Lindsay Willmore, Andrew J. Ballard, Joshua Bambrick, Sebastian W. Bodenstein, David A. Evans, Chia-Chun Hung, Michael O’Neill, David Reiman, Kathryn Tunyasuvunakool, Zachary Wu, Akvilė Žemgulytė, Eirini Arvaniti, Charles Beattie, Ottavia Bertolli, Alex Bridgland, Alexey Cherepanov, Miles Congreve, Alexander I. Cowen-Rivers, Andrew Cowie, Michael Figurnov, Fabian B. Fuchs, Hannah Gladman, Rishub Jain, Yousuf A. Khan, Caroline M. R. Low, Kuba Perlin, Anna Potapenko, Pascal Savy, Sukhdeep Singh, Adrian Stecula, Ashok Thillaisundaram, Catherine Tong, Sergei Yakneen, Ellen D. Zhong, Michal Zielinski, Augustin Žídek, Victor Bapst, Pushmeet Kohli, Max Jaderberg (), Demis Hassabis () and John M. Jumper ()
Additional contact information
Josh Abramson: Google DeepMind
Jonas Adler: Google DeepMind
Jack Dunger: Google DeepMind
Richard Evans: Google DeepMind
Tim Green: Google DeepMind
Alexander Pritzel: Google DeepMind
Olaf Ronneberger: Google DeepMind
Lindsay Willmore: Google DeepMind
Andrew J. Ballard: Google DeepMind
Joshua Bambrick: Isomorphic Labs
Sebastian W. Bodenstein: Google DeepMind
David A. Evans: Google DeepMind
Chia-Chun Hung: Isomorphic Labs
Michael O’Neill: Google DeepMind
David Reiman: Google DeepMind
Kathryn Tunyasuvunakool: Google DeepMind
Zachary Wu: Google DeepMind
Akvilė Žemgulytė: Google DeepMind
Eirini Arvaniti: Google DeepMind
Charles Beattie: Google DeepMind
Ottavia Bertolli: Google DeepMind
Alex Bridgland: Google DeepMind
Alexey Cherepanov: Isomorphic Labs
Miles Congreve: Isomorphic Labs
Alexander I. Cowen-Rivers: Google DeepMind
Andrew Cowie: Google DeepMind
Michael Figurnov: Google DeepMind
Fabian B. Fuchs: Google DeepMind
Hannah Gladman: Google DeepMind
Rishub Jain: Google DeepMind
Yousuf A. Khan: Google DeepMind
Caroline M. R. Low: Isomorphic Labs
Kuba Perlin: Google DeepMind
Anna Potapenko: Google DeepMind
Pascal Savy: Isomorphic Labs
Sukhdeep Singh: Google DeepMind
Adrian Stecula: Isomorphic Labs
Ashok Thillaisundaram: Google DeepMind
Catherine Tong: Isomorphic Labs
Sergei Yakneen: Isomorphic Labs
Ellen D. Zhong: Google DeepMind
Michal Zielinski: Google DeepMind
Augustin Žídek: Google DeepMind
Victor Bapst: Google DeepMind
Pushmeet Kohli: Google DeepMind
Max Jaderberg: Isomorphic Labs
Demis Hassabis: Google DeepMind
John M. Jumper: Google DeepMind

Nature, 2024, vol. 630, issue 8016, 493-500

Abstract: 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 design2–6. 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.2.37,8. Together, these results show that high-accuracy modelling across biomolecular space is possible within a single unified deep-learning framework.

Date: 2024
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Citations: View citations in EconPapers (43)

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DOI: 10.1038/s41586-024-07487-w

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