Institute for Protein Design

David Baker, PhD

Professor, HHMI Investigator, and Head of the Institute for Protein Design

David Baker, PhD, is Professor of Biochemistry, Director of the Institute for Protein Design, Investigator of the Howard Hughes Medical Institute, and adjunct professor of Genome Sciences, Bioengineering, Chemical Engineering, Computer Science, and Physics at the University of Washington. He received his Ph.D. degree in biochemistry with Randy Schekman at the University of California, Berkeley and did postdoctoral work in biophysics with David Agard at UCSF.  His research group is focused on the prediction and design of macromolecular structures, interactions and functions.  Dr. Baker received young investigator awards from the National Science Foundation and the Beckman Foundation, and the Packard Foundation fellowship in Science and Engineering.  He has also received the Irving Sigal Young Investigator award from the Protein Society and the Overton Prize from the International Society of Computational Biology.  He is a recipient of the Feynman Prize from the Foresight Institute, the AAAS Newcomb_Cleveland prize, the Sackler prize in biophysics, and the Centenary award from the Biochemical society. He is a member of the National Academy of Sciences and the American Academy of Sciences.  His research group is a world leader in computational protein design and protein structure prediction.


  • 2012 Biochemical Society Centenary Award
  • 2009 Sackler Prize in Biophysics
  • 2008 American Academy of Sciences
  • 2007 Editorial Board, PNAS
  • 2006 National Academy of Sciences
  • 2004 Foresight Institute Feynman Prize
  • 2004 AAAS Newcomb-Cleveland prize
  • 2003 Director, Biomolecular structure and design graduate program (BMSD
  • 2002 International Society for Computational Biology Overton Prize
  • 2000 Protein Society Young Investigator Award
  • 2000 HHMI Assistant Investigator
  • 2000 Editorial Advisory Board, Protein Science
  • 1995 Beckman Young Investigator Award
  • 1994 Packard Fellowship in Science and Engineering
  • 1994 National Science Foundation Young Investigator Award

Our research is focused on the prediction and design of protein structures, protein folding mechanisms, protein-protein interactions, protein-nucleotide interactions, and protein-ligand interactions. Our approach is to use experiments to understand the fundamental principles underlying these problems, to develop simple computational models based on these insights, and to test the models through structure prediction and design. We strive to continually improve our methodology by iterating between computational and experimental studies.