Predicting CD4 T-cell epitopes based on antigen cleavage, MHCII presentation, and TCR recognition

• Dina Schneidman-Duhovny ,

  Roles Conceptualization, Formal analysis, Investigation, Methodology, Software, Validation, Visualization, Writing – original draft, Writing – review & editing

  * E-mail: sali@salilab.org (AS); dina@salilab.org (DS); pedro.paz@bayer.com (PP); fred.aswad@bayer.com (FA)

  Current address: School of Computer Science and Engineering, Institute of Life Sciences, The Hebrew University of Jerusalem, Jerusalem, Israel

  Affiliations Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, United States of America, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, United States of America

  http://orcid.org/0000-0003-0480-0438

  ⨯
• Natalia Khuri,

  Roles Software, Validation, Writing – original draft, Writing – review & editing

  Affiliations Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, United States of America, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, United States of America, Graduate Group in Biophysics, University of California at San Francisco, San Francisco, CA, United States of America

  ⨯
• Guang Qiang Dong,

  Roles Data curation, Methodology, Software, Writing – review & editing

  Affiliations Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, United States of America, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, United States of America

  ⨯
• Michael B. Winter,

  Roles Data curation, Formal analysis, Methodology, Validation, Visualization, Writing – original draft, Writing – review & editing

  Affiliation Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, United States of America

  ⨯
• Eric Shifrut,

  Roles Data curation, Validation, Writing – review & editing

  Affiliation Department of Immunology, Weizmann Institute of Science, Rehovot, Israel

  ⨯
• Nir Friedman,

  Roles Data curation, Formal analysis, Methodology, Validation, Writing – review & editing

  Affiliation Department of Immunology, Weizmann Institute of Science, Rehovot, Israel

  ⨯
• Charles S. Craik,

  Roles Data curation, Validation, Visualization, Writing – original draft, Writing – review & editing

  Affiliations Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, United States of America, California Institute for Quantitative Biosciences (QB3), University of California, San Francisco, San Francisco, CA, United States of America

  ⨯
• Kathleen P. Pratt,

  Roles Data curation, Formal analysis, Validation, Writing – review & editing

  Affiliation Uniformed Services University of the Health Sciences, Bethesda, MD, United States of America

  ⨯
• Pedro Paz ,

  Roles Conceptualization, Data curation, Investigation, Validation, Writing – review & editing

  * E-mail: sali@salilab.org (AS); dina@salilab.org (DS); pedro.paz@bayer.com (PP); fred.aswad@bayer.com (FA)

  Affiliation Bayer HealthCare, San Francisco, CA, United States of America

  ⨯
• Fred Aswad ,

  Roles Data curation, Funding acquisition, Resources, Validation, Writing – review & editing

  * E-mail: sali@salilab.org (AS); dina@salilab.org (DS); pedro.paz@bayer.com (PP); fred.aswad@bayer.com (FA)

  Affiliation Bayer HealthCare, San Francisco, CA, United States of America

  http://orcid.org/0000-0001-9062-3735

  ⨯
• Andrej Sali

  Roles Conceptualization, Formal analysis, Funding acquisition, Investigation, Methodology, Supervision, Writing – original draft, Writing – review & editing

  * E-mail: sali@salilab.org (AS); dina@salilab.org (DS); pedro.paz@bayer.com (PP); fred.aswad@bayer.com (FA)

  Affiliations Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA, United States of America, Department of Pharmaceutical Chemistry, University of California, San Francisco, San Francisco, CA, United States of America, Graduate Group in Biophysics, University of California at San Francisco, San Francisco, CA, United States of America

  ⨯