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Accurate structure prediction of biomolecular interactions with AlphaFold 3

Author

Listed:
  • 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
    Stanford University)

  • 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
    Princeton University)

  • Michal Zielinski

    (Google DeepMind)

  • Augustin Žídek

    (Google DeepMind)

  • Victor Bapst

    (Google DeepMind)

  • Pushmeet Kohli

    (Google DeepMind)

  • Max Jaderberg

    (Isomorphic Labs)

  • Demis Hassabis

    (Google DeepMind
    Isomorphic Labs)

  • John M. Jumper

    (Google DeepMind)

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.

Suggested Citation

  • 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 , 2024. "Accurate structure prediction of biomolecular interactions with AlphaFold 3," Nature, Nature, vol. 630(8016), pages 493-500, June.
  • Handle: RePEc:nat:nature:v:630:y:2024:i:8016:d:10.1038_s41586-024-07487-w
    DOI: 10.1038/s41586-024-07487-w
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    Cited by:

    1. Cornelia Sala & Martin Würtz & Enrico Salvatore Atorino & Annett Neuner & Patrick Partscht & Thomas Hoffmann & Sebastian Eustermann & Elmar Schiebel, 2024. "An interaction network of inner centriole proteins organised by POC1A-POC1B heterodimer crosslinks ensures centriolar integrity," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
    2. Sanghyeon Choi & Youngjin Lee & Shinhye Park & Song Yee Jang & Jongbin Park & Do Won Oh & Su-Man Kim & Tae-Hwan Kim & Ga Seul Lee & Changyi Cho & Byoung Sik Kim & Donghan Lee & Eun-Hee Kim & Hae-Kap C, 2024. "Dissemination of pathogenic bacteria is reinforced by a MARTX toxin effector duet," Nature Communications, Nature, vol. 15(1), pages 1-20, December.
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    7. Yida Jiang & Xinghe Zhang & Honggang Nie & Jianxiong Fan & Shuangshuang Di & Hui Fu & Xiu Zhang & Lijuan Wang & Chun Tang, 2024. "Dissecting diazirine photo-reaction mechanism for protein residue-specific cross-linking and distance mapping," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
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    9. Qianqian Ming & Daniel Antfolk & David A. Price & Anna Manturova & Elliot Medina & Srishti Singh & Charlotte Mason & Timothy H. Tran & Keiran S. M. Smalley & Daisy W. Leung & Vincent C. Luca, 2024. "Structural basis for mouse LAG3 interactions with the MHC class II molecule I-Ab," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    10. Itxaso Anso & Samira Zouhir & Thibault Géry Sana & Petya Violinova Krasteva, 2024. "Structural basis for synthase activation and cellulose modification in the E. coli Type II Bcs secretion system," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    11. Huiyu Cai & Zuobai Zhang & Mingkai Wang & Bozitao Zhong & Quanxiao Li & Yuxuan Zhong & Yanling Wu & Tianlei Ying & Jian Tang, 2024. "Pretrainable geometric graph neural network for antibody affinity maturation," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    12. Marius Klein & Klemens Wild & Irmgard Sinning, 2024. "Multi-protein assemblies orchestrate co-translational enzymatic processing on the human ribosome," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    13. Juan M. Perez-Bertoldi & Yuanchang Zhao & Akanksha Thawani & Ahmet Yildiz & Eva Nogales, 2024. "HURP regulates Kif18A recruitment and activity to synergistically control microtubule dynamics," Nature Communications, Nature, vol. 15(1), pages 1-18, December.
    14. Yinghui Chen & Yunxin Xu & Di Liu & Yaoguang Xing & Haipeng Gong, 2024. "An end-to-end framework for the prediction of protein structure and fitness from single sequence," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    15. Lucas A. Defelipe & Katharina Veith & Osvaldo Burastero & Tatiana Kupriianova & Isabel Bento & Michal Skruzny & Knut Kölbel & Charlotte Uetrecht & Roland Thuenauer & Maria M. García-Alai, 2024. "Subtleties in Clathrin heavy chain binding boxes provide selectivity among adaptor proteins of budding yeast," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    16. Nathalie Béchon & Nitzan Tal & Avigail Stokar-Avihail & Alon Savidor & Meital Kupervaser & Sarah Melamed & Gil Amitai & Rotem Sorek, 2024. "Diversification of molecular pattern recognition in bacterial NLR-like proteins," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    17. Yijia Cheng & Mark A. B. Kreutzberger & Jianting Han & Edward H. Egelman & Qin Cao, 2024. "Molecular architecture of the assembly of Bacillus spore coat protein GerQ revealed by cryo-EM," Nature Communications, Nature, vol. 15(1), pages 1-10, December.
    18. Kenneth Bødkter Schou & Samuel Mandacaru & Muhammad Tahir & Nikola Tom & Ann-Sofie Nilsson & Jens S. Andersen & Matteo Tiberti & Elena Papaleo & Jiri Bartek, 2024. "Exploring the structural landscape of DNA maintenance proteins," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    19. Devlina Chakravarty & Joseph W. Schafer & Ethan A. Chen & Joseph F. Thole & Leslie A. Ronish & Myeongsang Lee & Lauren L. Porter, 2024. "AlphaFold predictions of fold-switched conformations are driven by structure memorization," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    20. Leishu Lin & Jiayuan Dong & Shun Xu & Jinman Xiao & Cong Yu & Fengfeng Niu & Zhiyi Wei, 2024. "Autoinhibition and relief mechanisms for MICAL monooxygenases in F-actin disassembly," Nature Communications, Nature, vol. 15(1), pages 1-14, December.
    21. Paloma García Casas & Michela Rossini & Linnea Påvénius & Mezida Saeed & Nikita Arnst & Sonia Sonda & Tânia Fernandes & Irene D’Arsiè & Matteo Bruzzone & Valeria Berno & Andrea Raimondi & Maria Livia , 2024. "Simultaneous detection of membrane contact dynamics and associated Ca2+ signals by reversible chemogenetic reporters," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
    22. Yang Yue & Shu Li & Yihua Cheng & Lie Wang & Tingjun Hou & Zexuan Zhu & Shan He, 2024. "Integration of molecular coarse-grained model into geometric representation learning framework for protein-protein complex property prediction," Nature Communications, Nature, vol. 15(1), pages 1-14, December.

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