About the Authors

Julia Koehler Leman

Contributed equally to this work with: Julia Koehler Leman, Brian D. Weitzner

julia.koehler.leman@gmail.com (JKL); bweitzner@lyell.com (BDW); jgray@jhu.edu (JJG); bonneau@nyu.edu (RB)

Affiliations Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, United States of America, Dept of Biology, New York University, New York, NY, United States of America

Brian D. Weitzner

Contributed equally to this work with: Julia Koehler Leman, Brian D. Weitzner

julia.koehler.leman@gmail.com (JKL); bweitzner@lyell.com (BDW); jgray@jhu.edu (JJG); bonneau@nyu.edu (RB)

Affiliations Dept of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, United States of America, Dept of Biochemistry, University of Washington, Seattle, WA, United States of America, Institute for Protein Design, University of Washington, Seattle, WA, United States of America, Lyell Immunopharma, Seattle, WA, United States of America

P. Douglas Renfrew

Affiliation Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, United States of America

Steven M. Lewis

Affiliations Dept of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America, Dept of Biochemistry, Duke University, Durham, NC, United States of America, Cyrus Biotechnology, Seattle, WA United States of America

Rocco Moretti

Affiliation Dept of Chemistry, Vanderbilt University, Nashville, TN, United States of America

Andrew M. Watkins

Affiliation Dept of Biochemistry, Stanford University School of Medicine, Stanford CA, United States of America

Vikram Khipple Mulligan

Affiliations Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, United States of America, Dept of Biochemistry, University of Washington, Seattle, WA, United States of America, Institute for Protein Design, University of Washington, Seattle, WA, United States of America

Sergey Lyskov

Affiliation Dept of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, United States of America

Jared Adolf-Bryfogle

Affiliation Dept of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States of America

Jason W. Labonte

Affiliations Dept of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, United States of America, Dept of Chemistry, Franklin & Marshall College, Lancaster, PA, United States of America

Justyna Krys

Affiliation Dept of Chemistry, University of Warsaw, Warsaw, Poland

RosettaCommons Consortium

Membership of the RosettaCommons Consortium is listed in the S1 List.

Christopher Bystroff

Affiliation Dept of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, United States of America

William Schief

Affiliation Dept of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, United States of America

Dominik Gront

Affiliation Dept of Chemistry, University of Warsaw, Warsaw, Poland

Ora Schueler-Furman

Affiliation Dept of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel

David Baker

Affiliations Dept of Biochemistry, University of Washington, Seattle, WA, United States of America, Institute for Protein Design, University of Washington, Seattle, WA, United States of America

Philip Bradley

Affiliation Fred Hutchinson Cancer Research Center, Seattle, WA, United States of America

Roland Dunbrack

Affiliation Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia PA, United States of America

Tanja Kortemme

Affiliation Dept of Bioengineering and Therapeutic Sciences, University of California San Francisco, CA, United States of America

Andrew Leaver-Fay

Affiliation Dept of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America

Charlie E. M. Strauss

Affiliation Bioscience Division, Los Alamos National Laboratory, Los Alamos, NM, United States of America

Jens Meiler

Affiliations Depts of Chemistry, Pharmacology and Biomedical Informatics, Vanderbilt University, Nashville, TN, United States of America, Center for Structural Biology, Vanderbilt University, Nashville, TN, United States of America, Institute for Chemical Biology, Vanderbilt University, Nashville, TN, United States of America, Institute for Drug Discovery, Leipzig University, Leipzig, Germany

Brian Kuhlman

Affiliation Dept of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, United States of America

Jeffrey J. Gray

julia.koehler.leman@gmail.com (JKL); bweitzner@lyell.com (BDW); jgray@jhu.edu (JJG); bonneau@nyu.edu (RB)

Affiliation Dept of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, United States of America

Richard Bonneau

julia.koehler.leman@gmail.com (JKL); bweitzner@lyell.com (BDW); jgray@jhu.edu (JJG); bonneau@nyu.edu (RB)

Affiliations Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, United States of America, Dept of Biology, New York University, New York, NY, United States of America, Dept of Computer Science, New York University, New York, NY, United States of America, Center for Data Science, New York University, New York, NY, United States of America

Competing Interests

The Rosetta software has been licensed to numerous non-profit and for-profit organizations. Rosetta Licensing is managed by UW CoMotion, and royalty proceeds are managed by the RosettaCommons. Under institutional participation agreements between the University of Washington, acting on behalf of the RosettaCommons, their respective institutions may be entitled to a portion of revenue received on licensing Rosetta software including programs described here. Baker, Malmström, Yarov-Yarovoy, Gront, Meiler, Whitehead, Schueler-Furman, King, Gray, Sgourakis, Lindert, Strauss, Karanicolas, Bonneau, Sammond, Kortemme, and Bradley are unpaid board members of the RosettaCommons. As members of the Scientific Advisory Board of Cyrus Biotechnology, Baker and Gray are granted stock options. Yifan Song, Indigo C. King, Steven M. Lewis, Brandon Frenz, Karen Khar and Ryan Pavlovicz are currently employed at Cyrus Biotechnology with granted stock options. Cyrus Biotechnology distributes the Rosetta software. Brian D. Weitzner and Scott E. Boyken hold equity in Lyell Immunopharma. Vikram K. Mulligan is a co-founder of and shareholder in Menten Biotechnology Labs, Inc. The content of this manuscript is relevant to work performed at Lyell and Menten. Neil P. King is a co-founder and shareholder of Icosavax, Inc., a biotech company developing nanoparticle vaccines. Justin B. Siegel is a co-founder and shareholder of Digestiva, Inc. and PvP Biologics Inc. David Baker is a co-founder, shareholder, or advisor to the following companies: ARZEDA, PvP Biologics, Cyrus Biotechnology, Cue Biopharma, Icosavax, Neoleukin Therapeutics, Lyell Immunotherapeutics, Sana Biotechnology, and A-Alpha Bio.