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Accurate prediction of protein structures and interactions using a three-track neural network.
Baek, Minkyung; DiMaio, Frank; Anishchenko, Ivan; Dauparas, Justas; Ovchinnikov, Sergey; Lee, Gyu Rie; Wang, Jue; Cong, Qian; Kinch, Lisa N; Schaeffer, R Dustin; Millán, Claudia; Park, Hahnbeom; Adams, Carson; Glassman, Caleb R; DeGiovanni, Andy; Pereira, Jose H; Rodrigues, Andria V; van Dijk, Alberdina A; Ebrecht, Ana C; Opperman, Diederik J; Sagmeister, Theo; Buhlheller, Christoph; Pavkov-Keller, Tea; Rathinaswamy, Manoj K; Dalwadi, Udit; Yip, Calvin K; Burke, John E; Garcia, K Christopher; Grishin, Nick V; Adams, Paul D; Read, Randy J; Baker, David.
Afiliação
  • Baek M; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
  • DiMaio F; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.
  • Anishchenko I; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
  • Dauparas J; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.
  • Ovchinnikov S; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
  • Lee GR; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.
  • Wang J; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
  • Cong Q; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.
  • Kinch LN; Faculty of Arts and Sciences, Division of Science, Harvard University, Cambridge, MA 02138, USA.
  • Schaeffer RD; John Harvard Distinguished Science Fellowship Program, Harvard University, Cambridge, MA 02138, USA.
  • Millán C; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
  • Park H; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.
  • Adams C; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
  • Glassman CR; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.
  • DeGiovanni A; Eugene McDermott Center for Human Growth and Development, University of Texas Southwestern Medical Center, Dallas, TX, USA.
  • Pereira JH; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
  • Rodrigues AV; Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX, USA.
  • van Dijk AA; Department of Biophysics, University of Texas Southwestern Medical Center, Dallas, TX, USA.
  • Ebrecht AC; Department of Haematology, Cambridge Institute for Medical Research, University of Cambridge, Cambridge, UK.
  • Opperman DJ; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
  • Sagmeister T; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.
  • Buhlheller C; Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
  • Pavkov-Keller T; Institute for Protein Design, University of Washington, Seattle, WA 98195, USA.
  • Rathinaswamy MK; Program in Immunology, Stanford University School of Medicine, Stanford, CA 94305, USA.
  • Dalwadi U; Department of Molecular and Cellular Physiology, Stanford University School of Medicine, Stanford, CA 94305, USA.
  • Yip CK; Department of Structural Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
  • Burke JE; Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
  • Garcia KC; Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
  • Grishin NV; Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.
  • Adams PD; Department of Biochemistry, Focus Area Human Metabolomics, North-West University, 2531 Potchefstroom, South Africa.
  • Read RJ; Department of Biochemistry, Focus Area Human Metabolomics, North-West University, 2531 Potchefstroom, South Africa.
  • Baker D; Department of Biotechnology, University of the Free State, 205 Nelson Mandela Drive, Bloemfontein 9300, South Africa.
Science ; 373(6557): 871-876, 2021 08 20.
Article em En | MEDLINE | ID: mdl-34282049
ABSTRACT
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.
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Texto completo: 1 Base de dados: MEDLINE Assunto principal: Conformação Proteica / Proteínas / Dobramento de Proteína / Aprendizado Profundo Idioma: En Ano de publicação: 2021 Tipo de documento: Article País de afiliação: Estados Unidos
Texto completo
Imprimir
XML
PubMed Links
Buscar no Google

Texto completo: 1 Base de dados: MEDLINE Assunto principal: Conformação Proteica / Proteínas / Dobramento de Proteína / Aprendizado Profundo Idioma: En Ano de publicação: 2021 Tipo de documento: Article País de afiliação: Estados Unidos