David Baker
David Baker
Head of the Institute for Protein Design
Professor of Biochemistry
Adjunct Professor of Bioengineering
Adjunct Professor of Genome Sciences
Adjunct Professor of Physics
Adjunct Professor of Chemical Engineering
Adjunct Professor of of Computer Science
Investigator, HHMI
BA 1984, Harvard University
PhD 1989, UC Berkeley
Off.: 422 MoIE
Ph.: 206.616.7542
Fax: 206.685.1792 (assistant)


  • 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

Baker Group website


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.

The successful application of our computational prediction and design method, ROSETTA, is illustrated in a few recent examples:

(i) We used computational protein design methods to create an artificial globular protein with a novel fold. Experimental characterization of Top7 showed that it is extremely stable, and the x-ray crystal structure is strikingly close to the design model. These results suggest that new proteins can be designed with atomic level accuracy, and current work is aimed at using these techniques to design new proteins with novel functions.

Top7: compare design and x-ray structure Comparisons of the Top7 design (green) and x-ray structure (yellow). (A) C-alpha overlay. (B) Overlay of core sidechains in the C-terminal portion.

(ii) We have redesigned protein-protein interaction specificity and demonstrated that the specificity changes hold both in vitro and in vivo.

Colicin E7/Im complex Backbone schematic of the colicin E7 DNase (teal) / Im7 Immunity protein (grey) complex. Important interfacial residues are shown in spacefill (E7 in red, Im7 in blue, conserved Tyr-Tyr motif in yellow).

(iii) Ab initio protein structure prediction. We produced de novo structure predictions of unprecedented accuracy in the recent CASP4 and CASP5 international blind tests of protein structure prediction methods. A more detailed description of our research can be found at


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