IDEAS home Printed from https://ideas.repec.org/a/nat/nature/v630y2024i8016d10.1038_s41586-024-07487-w.html
   My bibliography  Save this article

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
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41586-024-07487-w
    File Function: Abstract
    Download Restriction: Access to the full text of the articles in this series is restricted.

    File URL: https://libkey.io/10.1038/s41586-024-07487-w?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    As the access to this document is restricted, you may want to search for a different version of it.

    Citations

    Citations are extracted by the CitEc Project, subscribe to its RSS feed for this item.
    as


    Cited by:

    1. 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.
    2. 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.
    3. Tingting Li & Xuanbai Ren & Xiaoli Luo & Zhuole Wang & Zhenlu Li & Xiaoyan Luo & Jun Shen & Yun Li & Dan Yuan & Ruth Nussinov & Xiangxiang Zeng & Junfeng Shi & Feixiong Cheng, 2024. "A Foundation Model Identifies Broad-Spectrum Antimicrobial Peptides against Drug-Resistant Bacterial Infection," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    4. 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.
    5. 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.
    6. 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.
    7. 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.
    8. 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.
    9. 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.
    10. 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.
    11. 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.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:nature:v:630:y:2024:i:8016:d:10.1038_s41586-024-07487-w. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    We have no bibliographic references for this item. You can help adding them by using this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.