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2024年诺贝尔化学奖得主John M. Jumper AlphaFold3 2024年获奖论文分析报告

已有 1308 次阅读 2024-10-11 06:22 |个人分类:诺贝尔奖|系统分类:观点评述

 2024年诺贝尔化学奖得主John M. Jumper   AlphaFold3 2024年  当年论文获奖  

1. 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,John M Jumper

Core Contributor, Google DeepMind, London, UK.

jaderberg@isomorphiclabs.com

Nature (P 1476-4687 E 0028-0836) H指数：1096 2024 年 630 卷 8016 期 493-500 页

PMID：38718835 相似文献

文摘 DOI链接 Nature Publishing Group

http://www.pubmedplus.cn/P/SearchQuickResult?wd=6846f457-e1f5-48fa-9d58-474acf2e2587

陈德旺   38岁的诺奖得主给年轻人才成长的几点启示 精选

2018年开发的AlphaFold功能还比较弱，只能解析几十个蛋白质结构。 AlphaFold2于2020年面市，能在超过2亿个蛋白质结构中做出精准预测，大大解放了做蛋白质解析的科研人员。2024年5月的AlphaFold3，将蛋白质带入广泛的生物分子领域，为生物开发与药物设计、基因组学研究奠定了基础。

https://blog.sciencenet.cn/blog-57940-1454689.html

 2024年诺贝尔化学奖得主John M. Jumper   2024年 原文

https://pubmed.ncbi.nlm.nih.gov/38718835/

Nature

. 2024 Jun;630(8016):493-500.

 doi: 10.1038/s41586-024-07487-w. Epub 2024 May 8.

Accurate structure prediction of biomolecular interactions with AlphaFold 3

Josh Abramson # 1, Jonas Adler # 1, Jack Dunger # 1, Richard Evans # 1, Tim Green # 1, Alexander Pritzel # 1, Olaf Ronneberger # 1, Lindsay Willmore # 1, Andrew J Ballard 1, Joshua Bambrick 2, Sebastian W Bodenstein 1, David A Evans 1, Chia-Chun Hung 2, Michael O'Neill 1, David Reiman 1, Kathryn Tunyasuvunakool 1, Zachary Wu 1, Akvilė Žemgulytė 1, Eirini Arvaniti 3, Charles Beattie 3, Ottavia Bertolli 3, Alex Bridgland 3, Alexey Cherepanov 4, Miles Congreve 4, Alexander I Cowen-Rivers 3, Andrew Cowie 3, Michael Figurnov 3, Fabian B Fuchs 3, Hannah Gladman 3, Rishub Jain 3, Yousuf A Khan 3 5, Caroline M R Low 4, Kuba Perlin 3, Anna Potapenko 3, Pascal Savy 4, Sukhdeep Singh 3, Adrian Stecula 4, Ashok Thillaisundaram 3, Catherine Tong 4, Sergei Yakneen 4, Ellen D Zhong 3 6, Michal Zielinski 3, Augustin Žídek 3, Victor Bapst 1, Pushmeet Kohli 1, Max Jaderberg 7, Demis Hassabis 8 9, John M Jumper 10

Affiliations expand

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.

© 2024. The Author(s).

PubMed Disclaimer

Conflict of interest statement

Author-affiliated entities have filed US provisional patent applications including 63/611,674, 63/611,638 and 63/546,444 relating to predicting 3D structures of molecule complexes using embedding neural networks and generative models. All of the authors other than A.B., Y.A.K. and E.D.Z. have commercial interests in the work described.

Figures

Fig. 1

Fig. 1. AF3 accurately predicts structures across…

 Fig. 2

Fig. 2. Architectural and training details. 

a…

 Fig. 3

Fig. 3. Examples of predicted complexes. 

Selected…

 Fig. 4

Fig. 4. AF3 confidences track accuracy. 

a…

 Fig. 5

Fig. 5. Model limitations. 

a , Antibody…

 Extended Data Fig. 1

Extended Data Fig. 1. Disordered region prediction.

All figures (14)

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References

    1. Jumper J, et al. Highly accurate protein structure prediction with AlphaFold. Nature. 2021;596:583–589. - PMC - PubMed

    1. Kreitz J, et al. Programmable protein delivery with a bacterial contractile injection system. Nature. 2023;616:357–364. - PMC - PubMed

    1. Lim Y, et al. In silico protein interaction screening uncovers DONSON’s role in replication initiation. Science. 2023;381:eadi3448. - PMC - PubMed

    1. Mosalaganti S, et al. AI-based structure prediction empowers integrative structural analysis of human nuclear pores. Science. 2022;376:eabm9506. - PubMed

    1. Anand, N. & Achim, T. Protein structure and sequence generation with equivariant denoising diffusion probabilistic models. Preprint at arXiv10.48550/arXiv.2205.15019 (2022).

Show all 73 references

MeSH terms

  • Antibodies / chemistry

  • Antibodies / metabolism

  • Antigens / chemistry

  • Antigens / metabolism

  • Deep Learning* / standards

  • Humans

  • Ions / chemistry

  • Ions / metabolism

  • Ligands*

  • Models, Molecular*

  • Molecular Docking Simulation

  • Nucleic Acids / chemistry

  • Nucleic Acids / metabolism

  • Protein Binding

  • Protein Conformation

  • Proteins* / chemistry

  • Proteins* / metabolism

  • Reproducibility of Results

  • Software* / standards

Substances

  • Antibodies

  • Antigens

  • Ions

  • Ligands

  • Nucleic Acids

  • Proteins

Related informationLinkOut - more resources

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01.无法确认6 篇27.273%
02.20249 篇40.909%
01.biorxiv2 篇9.091%
02.int j biol macromol2 篇9.091%
03.nature2 篇9.091%
04.arxiv1 篇4.545%
05.bioinformatics1 篇4.545%
06.chembiochem1 篇4.545%
07.int j mol sci1 篇4.545%
08.j am chem soc1 篇4.545%
09.j chem inf model1 篇4.545%
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01.美国7 篇31.818%
02.加拿大3 篇13.636%
03.中国2 篇9.091%
04.奥地利1 篇4.545%
05.荷兰1 篇4.545%
06.瑞士1 篇4.545%
07.土耳其1 篇4.545%
01.中国上海1 篇4.545%
02.中国福州1 篇4.545%
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01.Protein Conformation6 篇27.273%
02.Protein Folding5 篇22.727%
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07.Artificial Intelligence2 篇9.091%
08.Computational Biology2 篇9.091%
09.Deep Learning2 篇9.091%
10.Humans2 篇9.091%

AlphaFold3 研究相似文献分析如下

1. 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,John M Jumper

Core Contributor, Google DeepMind, London, UK.

jaderberg@isomorphiclabs.com

Nature (P 1476-4687 E 0028-0836) H指数：1096 2024 年 630 卷 8016 期 493-500 页

PMID：38718835 相似文献

文摘 DOI链接 Nature Publishing Group

http://www.pubmedplus.cn/P/SearchQuickResult?wd=28b5032e-bd31-4b49-8e2a-a0e9f0266981

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20.20011 篇1.000%
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07.nucleic acids res4 篇4.000%
08.acc chem res3 篇3.000%
09.biorxiv3 篇3.000%
10.int j mol sci3 篇3.000%
01.美国38 篇38.000%
02.中国23 篇23.000%
03.英国9 篇9.000%
04.德国8 篇8.000%
05.日本5 篇5.000%
06.法国4 篇4.000%
07.韩国4 篇4.000%
08.加拿大4 篇4.000%
09.瑞典4 篇4.000%
10.瑞士4 篇4.000%
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04.中国北京2 篇2.000%
05.中国长春2 篇2.000%
06.中国上海2 篇2.000%
07.中国深圳2 篇2.000%
08.中国香港2 篇2.000%
09.中国哈尔滨1 篇1.000%
10.中国常州1 篇1.000%
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04.Ligands40 篇40.000%
05.Molecular Docking Simulation36 篇36.000%
06.Nucleic Acids34 篇34.000%
07.Models, Molecular29 篇29.000%
08.Software28 篇28.000%
09.Binding Sites21 篇21.000%
10.Deep Learning21 篇21.000%



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