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Accurate prediction of protein structures and interactions using a 3-track network

View ORCID ProfileMinkyung Baek, Frank DiMaio, View ORCID ProfileIvan Anishchenko, View ORCID ProfileJustas Dauparas, View ORCID ProfileSergey Ovchinnikov, Gyu Rie Lee, Jue Wang, View ORCID ProfileQian Cong, Lisa N. Kinch, R. Dustin Schaeffer, Claudia Millán, Hahnbeom Park, Carson Adams, Caleb R. Glassman, Andy DeGiovanni, Jose H. Pereira, Andria V. Rodrigues, Alberdina A. van Dijk, Ana C. Ebrecht, Diederik J. Opperman, Theo Sagmeister, Christoph Buhlheller, Tea Pavkov-Keller, Manoj K Rathinaswamy, Udit Dalwadi, Calvin K Yip, View ORCID ProfileJohn E Burke, K. Christopher Garcia, Nick V. Grishin, Paul D. Adams, Randy J. Read, David Baker
doi: https://doi.org/10.1101/2021.06.14.448402
Minkyung Baek
1Department of Biochemistry, University of Washington; Seattle, WA98195, USA
2Institute for Protein Design, University of Washington; Seattle, WA98195, USA
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Frank DiMaio
1Department of Biochemistry, University of Washington; Seattle, WA98195, USA
2Institute for Protein Design, University of Washington; Seattle, WA98195, USA
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Ivan Anishchenko
1Department of Biochemistry, University of Washington; Seattle, WA98195, USA
2Institute for Protein Design, University of Washington; Seattle, WA98195, USA
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Justas Dauparas
1Department of Biochemistry, University of Washington; Seattle, WA98195, USA
2Institute for Protein Design, University of Washington; Seattle, WA98195, USA
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Sergey Ovchinnikov
3Faculty of Arts and Sciences, Division of Science, Harvard University; Cambridge, MA02138, USA
4John Harvard Distinguished Science Fellowship Program, Harvard University; Cambridge, MA 02138, USA
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Gyu Rie Lee
1Department of Biochemistry, University of Washington; Seattle, WA98195, USA
2Institute for Protein Design, University of Washington; Seattle, WA98195, USA
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Jue Wang
1Department of Biochemistry, University of Washington; Seattle, WA98195, USA
2Institute for Protein Design, University of Washington; Seattle, WA98195, USA
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Qian Cong
5Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center; Dallas, TX, USA
6Department of Biophysics, University of Texas Southwestern Medical Center; Dallas, TX, USA
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Lisa N. Kinch
8Howard Hughes Medical Institute, University of Texas Southwestern Medical Center; Dallas, TX, USA
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R. Dustin Schaeffer
6Department of Biophysics, University of Texas Southwestern Medical Center; Dallas, TX, USA
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Claudia Millán
9Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge; Cambridge, U.K.
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Hahnbeom Park
1Department of Biochemistry, University of Washington; Seattle, WA98195, USA
2Institute for Protein Design, University of Washington; Seattle, WA98195, USA
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Carson Adams
1Department of Biochemistry, University of Washington; Seattle, WA98195, USA
2Institute for Protein Design, University of Washington; Seattle, WA98195, USA
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Caleb R. Glassman
10Program in Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
11Departments of Molecular and Cellular Physiology and Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
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Andy DeGiovanni
12Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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Jose H. Pereira
12Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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Andria V. Rodrigues
12Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
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Alberdina A. van Dijk
13Department of Biochemistry, North-West University; 2531 Potchefstroom, South Africa
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Ana C. Ebrecht
13Department of Biochemistry, North-West University; 2531 Potchefstroom, South Africa
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Diederik J. Opperman
14Department of Biotechnology, University of the Free State; 205 Nelson Mandela Drive, Bloemfontein, 9300, South Africa
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Theo Sagmeister
15Institute of Molecular Biosciences, University of Graz; Humboldtstrasse 50, 8010, Graz, Austria
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Christoph Buhlheller
15Institute of Molecular Biosciences, University of Graz; Humboldtstrasse 50, 8010, Graz, Austria
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Tea Pavkov-Keller
15Institute of Molecular Biosciences, University of Graz; Humboldtstrasse 50, 8010, Graz, Austria
16BioTechMed-Graz; Graz, Austria
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Manoj K Rathinaswamy
17Department of Biochemistry and Microbiology, University of Victoria; Victoria, British Columbia, Canada
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Udit Dalwadi
17Department of Biochemistry and Microbiology, University of Victoria; Victoria, British Columbia, Canada
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Calvin K Yip
17Department of Biochemistry and Microbiology, University of Victoria; Victoria, British Columbia, Canada
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John E Burke
17Department of Biochemistry and Microbiology, University of Victoria; Victoria, British Columbia, Canada
18Life Sciences Institute, Department of Biochemistry and Molecular Biology, University of British Columbia; Vancouver, British Columbia, Canada
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K. Christopher Garcia
19Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
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Nick V. Grishin
6Department of Biophysics, University of Texas Southwestern Medical Center; Dallas, TX, USA
7Department of Biochemistry, University of Texas Southwestern Medical Center; Dallas, TX, USA
8Howard Hughes Medical Institute, University of Texas Southwestern Medical Center; Dallas, TX, USA
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Paul D. Adams
10Program in Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA
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Randy J. Read
9Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge; Cambridge, U.K.
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David Baker
1Department of Biochemistry, University of Washington; Seattle, WA98195, USA
2Institute for Protein Design, University of Washington; Seattle, WA98195, USA
20Howard Hughes Medical Institute, University of Washington; Seattle, WA98195, USA
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  • For correspondence: dabaker@uw.edu
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Abstract

DeepMind presented remarkably accurate protein structure predictions at the CASP14 conference. We explored network architectures incorporating related ideas and obtained the best performance with a 3-track network in which information at the 1D sequence level, the 2D distance map level, and the 3D coordinate level is successively transformed and integrated. The 3-track network produces structure predictions with accuracies approaching those of DeepMind in CASP14, enables rapid solution of challenging X-ray crystallography and cryo-EM structure modeling problems, and provides insights into the functions of proteins of currently unknown structure. The network also enables rapid generation of accurate models of protein-protein complexes from sequence information alone, short circuiting traditional approaches which require modeling of individual subunits followed by docking. We make the method available to the scientific community to speed biological research.

One-Sentence Summary Accurate protein structure modeling enables rapid solution of structure determination problems and provides insights into biological function.

Competing Interest Statement

The authors have declared no competing interest.

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The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted June 15, 2021.
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Accurate prediction of protein structures and interactions using a 3-track network
Minkyung Baek, Frank DiMaio, Ivan Anishchenko, Justas Dauparas, Sergey Ovchinnikov, Gyu Rie Lee, Jue Wang, Qian Cong, Lisa N. Kinch, R. Dustin Schaeffer, Claudia Millán, Hahnbeom Park, Carson Adams, Caleb R. Glassman, Andy DeGiovanni, Jose H. Pereira, Andria V. Rodrigues, Alberdina A. van Dijk, Ana C. Ebrecht, Diederik J. Opperman, Theo Sagmeister, Christoph Buhlheller, Tea Pavkov-Keller, Manoj K Rathinaswamy, Udit Dalwadi, Calvin K Yip, John E Burke, K. Christopher Garcia, Nick V. Grishin, Paul D. Adams, Randy J. Read, David Baker
bioRxiv 2021.06.14.448402; doi: https://doi.org/10.1101/2021.06.14.448402
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Accurate prediction of protein structures and interactions using a 3-track network
Minkyung Baek, Frank DiMaio, Ivan Anishchenko, Justas Dauparas, Sergey Ovchinnikov, Gyu Rie Lee, Jue Wang, Qian Cong, Lisa N. Kinch, R. Dustin Schaeffer, Claudia Millán, Hahnbeom Park, Carson Adams, Caleb R. Glassman, Andy DeGiovanni, Jose H. Pereira, Andria V. Rodrigues, Alberdina A. van Dijk, Ana C. Ebrecht, Diederik J. Opperman, Theo Sagmeister, Christoph Buhlheller, Tea Pavkov-Keller, Manoj K Rathinaswamy, Udit Dalwadi, Calvin K Yip, John E Burke, K. Christopher Garcia, Nick V. Grishin, Paul D. Adams, Randy J. Read, David Baker
bioRxiv 2021.06.14.448402; doi: https://doi.org/10.1101/2021.06.14.448402

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