Accurate prediction of protein structures and interactions using a three-track neural network

被引：3205

作者：

Baek, Minkyung ^{[1
,2
]}

DiMaio, Frank ^{[1
,2
]}

Anishchenko, Ivan ^{[1
,2
]}

Dauparas, Justas ^{[1
,2
]}

Ovchinnikov, Sergey ^{[3
,4
]}

Lee, Gyu Rie ^{[1
,2
]}

Wang, Jue ^{[1
,2
]}

Cong, Qian ^{[5
,6
]}

Kinch, Lisa N. ^{[7
]}

Schaeffer, R. Dustin ^{[6
]}

Millan, Claudia ^{[8
]}

Park, Hahnbeom ^{[1
,2
]}

Adams, Carson ^{[1
,2
]}

Glassman, Caleb R. ^{[9
,10
,11
]}

DeGiovanni, Andy ^{[12
]}

Pereira, Jose H. ^{[12
]}

Rodrigues, Andria V. ^{[12
]}

van Dijk, Alberdina A. ^{[13
]}

Ebrecht, Ana C. ^{[13
]}

Opperman, Diederik J. ^{[14
]}

Sagmeister, Theo ^{[15
]}

Buhlheller, Christoph ^{[15
,16
]}

Pavkov-Keller, Tea ^{[15
,17
]}

Rathinaswamy, Manoj K. ^{[18
]}

Dalwadi, Udit ^{[19
]}

Yip, Calvin K. ^{[19
]}

Burke, John E. ^{[18
]}

Garcia, K. Christopher ^{[9
,10
,11
,20
]}

Grishin, Nick V. ^{[6
,7
,21
]}

Adams, Paul D. ^{[12
,22
]}

Read, Randy J. ^{[8
]}

Baker, David ^{[1
,2
,23
]}

机构：

[1] Univ Washington, Dept Biochem, Seattle, WA 98195 USA

[2] Univ Washington, Inst Prot Design, Seattle, WA 98195 USA

[3] Harvard Univ, Div Sci, Fac Arts & Sci, Cambridge, MA 02138 USA

[4] Harvard Univ, John Harvard Distinguished Sci Fellowship Program, Cambridge, MA 02138 USA

[5] Univ Texas Southwestern Med Ctr Dallas, Eugene McDermott Ctr Human Growth & Dev, Dallas, TX 75390 USA

[6] Univ Texas Southwestern Med Ctr Dallas, Dept Phys, Dallas, TX 75390 USA

[7] Univ Texas Southwestern Med Ctr Dallas, Howard Hughes Med Inst, Dallas, TX USA

[8] Univ Cambridge, Cambridge Inst Med Res, Dept Haematol, Cambridge, England

[9] Stanford Univ, Sch Med, Program Immunol, Stanford, CA 94305 USA

[10] Stanford Univ, Sch Med, Dept Mol & Cellular Physiol, Stanford, CA 94305 USA

[11] Stanford Univ, Sch Med, Dept Biol Struct, Stanford, CA 94305 USA

[12] Lawrence Berkeley Natl Lab, Mol Biophys & Integrated Bioimaging Div, Berkeley, CA USA

[13] North West Univ, Dept Biochem, Focus Area Human Metabol, ZA-2531 Potchefstroom, South Africa

[14] Univ Free State, Dept Biotechnol, 205 Nelson Mandela Dr, ZA-9300 Bloemfontein, South Africa

[15] Karl Franzens Univ Graz, Inst Mol Biosci, Humboldtstr 50, A-8010 Graz, Austria

[16] Med Univ Graz, Graz, Austria

[17] BioTechMed Graz, Graz, Austria

[18] Univ Victoria, Dept Biochem & Microbiol, Victoria, BC, Canada

[19] Univ British Columbia, Life Sci Inst, Dept Biochem & Mol Biol, Vancouver, BC, Canada

[20] Stanford Univ, Howard Hughes Med Inst, Sch Med, Stanford, CA 94305 USA

[21] Univ Texas Southwestern Med Ctr Dallas, Dept Biochem, Dallas, TX 75390 USA

[22] Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA

[23] Univ Washington, Howard Hughes Med Inst, Seattle, WA 98195 USA

来源：

SCIENCE | 2021年 / 373卷 / 6557期

基金：

英国惠康基金; 奥地利科学基金会; 美国国家卫生研究院; 美国国家科学基金会;

关键词：

MULTIPLE SEQUENCE ALIGNMENT; MOLECULAR-REPLACEMENT; STRUCTURE REFINEMENT; CRYSTAL-STRUCTURES; METABOLIC CRISES; FAMILY; MODELS; DOMAIN; DISINTEGRIN; FEATURES;

D O I：

10.1126/science.abj8754

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

DeepMind presented notably accurate predictions at the recent 14th Critical Assessment of Structure Prediction (CASP14) conference. We explored network architectures that incorporate related ideas and obtained the best performance with a three-track network in which information at the one-dimensional (1D) sequence level, the 2D distance map level, and the 3D coordinate level is successively transformed and integrated. The three-track network produces structure predictions with accuracies approaching those of DeepMind in CASP14, enables the rapid solution of challenging x-ray crystallography and cryo-electron microscopy structure modeling problems, and provides insights into the functions of proteins of currently unknown structure. The network also enables rapid generation of accurate protein-protein complex models from sequence information alone, short-circuiting traditional approaches that require modeling of individual subunits followed by docking. We make the method available to the scientific community to speed biological research.

引用

页码：871 / +

页数：52

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