Macromolecular modeling and design in Rosetta: recent methods and frameworks

Affiliations

• ¹ Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA. Julia.koehler.leman@nyu.edu.
• ² Department of Biology, New York University, New York, New York, USA. Julia.koehler.leman@nyu.edu.
• ³ Department of Chemical and Biomolecular Engineering, Johns Hopkins University, Baltimore, MD, USA.
• ⁴ Department of Biochemistry, University of Washington, Seattle, WA, USA.
• ⁵ Institute for Protein Design, University of Washington, Seattle, WA, USA.
• ⁶ Lyell Immunopharma Inc., Seattle, WA, USA.
• ⁷ Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
• ⁸ Department of Biochemistry, Duke University, Durham, NC, USA.
• ⁹ Cyrus Biotechnology, Seattle, WA, USA.
• ¹⁰ Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA.
• ¹¹ Department of Microbiology and Molecular Genetics, IMRIC, Ein Kerem Faculty of Medicine, Hebrew University of Jerusalem, Jerusalem, Israel.
• ¹² Department of Chemistry and Biochemistry, Ohio State University, Columbus, OH, USA.
• ¹³ Graduate Program in Bioinformatics, University of California San Francisco, San Francisco, CA, USA.
• ¹⁴ Institute of Bioengineering, École Polytechnique Fédérale de Lausanne, Lausanne, Switzerland.
• ¹⁵ Baylor College of Medicine, Department of Pharmacology, Houston, TX, USA.
• ¹⁶ Biological Physics Structure and Design PhD Program, University of Washington, Seattle, WA, USA.
• ¹⁷ Department of Pharmacology, Vanderbilt University, Nashville, TN, USA.
• ¹⁸ Institute of Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
• ¹⁹ Swiss Institute of Bioinformatics, Lausanne, Switzerland.
• ²⁰ Fred Hutchinson Cancer Research Center, Seattle, WA, USA.
• ²¹ Department of Biological Sciences, Rensselaer Polytechnic Institute, Troy, NY, USA.
• ²² Khoury College of Computer Sciences, Northeastern University, Boston, MA, USA.
• ²³ Department of Biochemistry, Stanford University School of Medicine, Stanford, CA, USA.
• ²⁴ DSM Biotechnology Center, Delft, the Netherlands.
• ²⁵ Institute for Cancer Research, Fox Chase Cancer Center, Philadelphia, PA, USA.
• ²⁶ Department of Chemistry, Vanderbilt University, Nashville, TN, USA.
• ²⁷ University of Maryland Institute for Bioscience and Biotechnology Research, Rockville, MD, USA.
• ²⁸ Department of Cell Biology and Molecular Genetics, University of Maryland, College Park, MD, USA.
• ²⁹ Program in Molecular Biophysics, Johns Hopkins University, Baltimore, MD, USA.
• ³⁰ Faculty of Chemistry, Biological and Chemical Research Centre, University of Warsaw, Warsaw, Poland.
• ³¹ Department of Chemistry & Biochemistry, University of Denver, Denver, CO, USA.
• ³² The Knoebel Institute for Healthy Aging, University of Denver, Denver, CO, USA.
• ³³ Research School of Chemistry, Australian National University, Canberra, Australian Capital Territory, Australia.
• ³⁴ Program in Bioinformatics and Computational Biology, Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA.
• ³⁵ Center for Computational Biology, University of Kansas, Lawrence, KS, USA.
• ³⁶ Biophysics Program, Stanford University, Stanford, CA, USA.
• ³⁷ Institute for Computational Science, University of Zurich, Zurich, Switzerland.
• ³⁸ S3IT, University of Zurich, Zurich, Switzerland.
• ³⁹ Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
• ⁴⁰ Department of Chemistry and Chemical Biology, The State University of New Jersey, Piscataway, NJ, USA.
• ⁴¹ Center for Integrative Proteomics Research, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
• ⁴² Computational Biology and Molecular Biophysics Program, Rutgers, The State University of New Jersey, Piscataway, NJ, USA.
• ⁴³ Department of Computer and Information Science, University of Massachusetts Dartmouth, Dartmouth, MA, USA.
• ⁴⁴ Department of Bioengineering and Therapeutic Sciences, University of California San Francisco, San Francisco, CA, USA.
• ⁴⁵ Center for Structural Biology, Vanderbilt University, Nashville, TN, USA.
• ⁴⁶ Medical Device Development and Regulation Research Center, School of Engineering, University of Tokyo, Tokyo, Japan.
• ⁴⁷ Department of Bioengineering, School of Engineering, University of Tokyo, Tokyo, Japan.
• ⁴⁸ Department of Chemistry, Franklin & Marshall College, Lancaster, PA, USA.
• ⁴⁹ Department of Biomolecular Sciences, Weizmann Institute of Science, Rehovot, Israel.
• ⁵⁰ Division of Infection Medicine, Department of Clinical Sciences Lund, Faculty of Medicine, Lund University, Lund, Sweden.
• ⁵¹ Institute for Research in Biomedicine Barcelona, The Barcelona Institute of Science and Technology, Barcelona, Spain.
• ⁵² Departments of Chemistry, Pharmacology and Biomedical Informatics, Vanderbilt University, Nashville, TN, USA.
• ⁵³ Institute for Chemical Biology, Vanderbilt University, Nashville, TN, USA.
• ⁵⁴ Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA.
• ⁵⁵ Department of Computer Science, University of California Santa Cruz, Santa Cruz, CA, USA.
• ⁵⁶ Molecular and Cellular Biology Program, University of Washington, Seattle, WA, USA.
• ⁵⁷ Chemical and Physical Biology Program, Vanderbilt Vaccine Center, Vanderbilt University, Nashville, TN, USA.
• ⁵⁸ Department of Chemistry and Biochemistry, University of California Santa Cruz, Santa Cruz, CA, USA.
• ⁵⁹ Department of Chemistry, University of California, Davis, Davis, CA, USA.
• ⁶⁰ Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, California, USA.
• ⁶¹ Genome Center, University of California, Davis, Davis, CA, USA.
• ⁶² Center for Computational Biology, Flatiron Institute, Simons Foundation, New York, NY, USA. Bonneau@nyu.edu.
• ⁶³ Department of Biology, New York University, New York, New York, USA. Bonneau@nyu.edu.
• ⁶⁴ Department of Computer Science, New York University, New York, NY, USA. Bonneau@nyu.edu.
• ⁶⁵ Center for Data Science, New York University, New York, NY, USA. Bonneau@nyu.edu.