Deep learning methods for designing proteins scaffolding functional sites

Jue Wang; Sidney Lisanza; David Juergens; Doug Tischer; Ivan Anishchenko; Minkyung Baek; Joseph L. Watson; Jung Ho Chun; Lukas F. Milles; Justas Dauparas; Marc Expòsit; Wei Yang; Amijai Saragovi; Sergey Ovchinnikov; David Baker

doi:10.1101/2021.11.10.468128

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Deep learning methods for designing proteins scaffolding functional sites

View ORCID ProfileJue Wang, Sidney Lisanza, View ORCID ProfileDavid Juergens, View ORCID ProfileDoug Tischer, View ORCID ProfileIvan Anishchenko, View ORCID ProfileMinkyung Baek, View ORCID ProfileJoseph L. Watson, Jung Ho Chun, View ORCID ProfileLukas F. Milles, View ORCID ProfileJustas Dauparas, Marc Expòsit, Wei Yang, View ORCID ProfileAmijai Saragovi, View ORCID ProfileSergey Ovchinnikov, View ORCID ProfileDavid Baker

doi: https://doi.org/10.1101/2021.11.10.468128

Jue Wang

aDepartment of Biochemistry, University of Washington, Seattle, WA 98105, USA

bInstitute for Protein Design, University of Washington, Seattle, WA 98105, USA

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ORCID record for Jue Wang

Sidney Lisanza

aDepartment of Biochemistry, University of Washington, Seattle, WA 98105, USA

bInstitute for Protein Design, University of Washington, Seattle, WA 98105, USA

cGraduate program in Biological Physics, Structure and Design, University of Washington, Seattle, WA 98105, USA

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David Juergens

aDepartment of Biochemistry, University of Washington, Seattle, WA 98105, USA

bInstitute for Protein Design, University of Washington, Seattle, WA 98105, USA

gGraduate program in Molecular Engineering, University of Washington, Seattle, WA 98105, USA

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ORCID record for David Juergens

Doug Tischer

aDepartment of Biochemistry, University of Washington, Seattle, WA 98105, USA

bInstitute for Protein Design, University of Washington, Seattle, WA 98105, USA

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ORCID record for Doug Tischer

Ivan Anishchenko

aDepartment of Biochemistry, University of Washington, Seattle, WA 98105, USA

bInstitute for Protein Design, University of Washington, Seattle, WA 98105, USA

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ORCID record for Ivan Anishchenko

Minkyung Baek

aDepartment of Biochemistry, University of Washington, Seattle, WA 98105, USA

bInstitute for Protein Design, University of Washington, Seattle, WA 98105, USA

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ORCID record for Minkyung Baek

Joseph L. Watson

aDepartment of Biochemistry, University of Washington, Seattle, WA 98105, USA

bInstitute for Protein Design, University of Washington, Seattle, WA 98105, USA

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ORCID record for Joseph L. Watson

Jung Ho Chun

aDepartment of Biochemistry, University of Washington, Seattle, WA 98105, USA

bInstitute for Protein Design, University of Washington, Seattle, WA 98105, USA

cGraduate program in Biological Physics, Structure and Design, University of Washington, Seattle, WA 98105, USA

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Lukas F. Milles

aDepartment of Biochemistry, University of Washington, Seattle, WA 98105, USA

bInstitute for Protein Design, University of Washington, Seattle, WA 98105, USA

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ORCID record for Lukas F. Milles

Justas Dauparas

aDepartment of Biochemistry, University of Washington, Seattle, WA 98105, USA

bInstitute for Protein Design, University of Washington, Seattle, WA 98105, USA

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ORCID record for Justas Dauparas

Marc Expòsit

aDepartment of Biochemistry, University of Washington, Seattle, WA 98105, USA

bInstitute for Protein Design, University of Washington, Seattle, WA 98105, USA

gGraduate program in Molecular Engineering, University of Washington, Seattle, WA 98105, USA

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Wei Yang

aDepartment of Biochemistry, University of Washington, Seattle, WA 98105, USA

bInstitute for Protein Design, University of Washington, Seattle, WA 98105, USA

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Amijai Saragovi

aDepartment of Biochemistry, University of Washington, Seattle, WA 98105, USA

bInstitute for Protein Design, University of Washington, Seattle, WA 98105, USA

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ORCID record for Amijai Saragovi

Sergey Ovchinnikov

dFAS Division of Science, Harvard University, Cambridge, MA 02138, USA

eJohn Harvard Distinguished Science Fellowship Program, Harvard University, Cambridge, MA 02138, USA

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ORCID record for Sergey Ovchinnikov
For correspondence: dabaker@uw.edu so@fas.harvard.edu

David Baker

aDepartment of Biochemistry, University of Washington, Seattle, WA 98105, USA

bInstitute for Protein Design, University of Washington, Seattle, WA 98105, USA

fHoward Hughes Medical Institute, University of Washington, Seattle, WA 98105, USA

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ORCID record for David Baker
For correspondence: dabaker@uw.edu so@fas.harvard.edu

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Deep learning methods for designing proteins scaffolding functional sites

Jue Wang, Sidney Lisanza, David Juergens, Doug Tischer, Ivan Anishchenko, Minkyung Baek, Joseph L. Watson, Jung Ho Chun, Lukas F. Milles, Justas Dauparas, Marc Expòsit, Wei Yang, Amijai Saragovi, Sergey Ovchinnikov, David Baker

bioRxiv 2021.11.10.468128; doi: https://doi.org/10.1101/2021.11.10.468128

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Deep learning methods for designing proteins scaffolding functional sites

bioRxiv 2021.11.10.468128; doi: https://doi.org/10.1101/2021.11.10.468128

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