David Baker (biochemist)

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David Baker
David Baker at the summit of Spark Plug Mountain, Washington, July 31, 2013
David Baker at the summit of Spark Plug Mountain, Washington, July 31, 2013
Born (1962-10-06) October 6, 1962 (age 55)
Alma mater
Known for
Spouse(s) Hannele Ruohola-Baker
Scientific career
Fields computational biologist
Doctoral advisor Randy Schekman
Other academic advisors David Agard
Website www.bakerlab.org

David Baker (born October 6, 1962 in Seattle, Washington[citation needed]) is an American biochemist and computational biologist who has pioneered methods to predict and design the three-dimensional structures of proteins. He is a Professor of Biochemistry at the University of Washington (UW),[1] where he is the principal investigator of the 80+ member Baker laboratory. He serves as the Director and Safety Officer of the Rosetta Commons, a consortium of labs and researchers that develop biomolecular structure prediction and design software. He is a Howard Hughes Medical Institute investigator and a member of the United States National Academy of Sciences.[2][3][4][5][6][7][8]


The Baker laboratory developed the Rosetta algorithm for ab initio protein structure prediction, which has been extended to a distributed computing project called [email protected][9] and Foldit.[10][11] The project aims to produce structural models for protein complexes as well as individual polypeptide chains. The Baker group participates regularly and is recognized for expertise in the CASP structure prediction experiment using ab initio methods, including both manually assisted and automated variants of the Rosetta protocol.[12][13]

Members of the Baker group are also active in the field of protein design; they are recognized as the first group to have designed a protein, known as Top7, with an entirely novel fold.[14]

Baker did his graduate work in biochemistry at the University of California, Berkeley in the laboratory of Randy Schekman, where he worked predominantly on protein transport and trafficking in yeast. He did his postdoctoral work with David Agard of University of California, San Francisco.

Although well known for development of methods for computational prediction of protein structure and function, Baker is focused on the use of computational methods to drive experimental assessment of biology and therefore the Baker laboratory maintains an active experimental biochemistry group.

For his work on protein folding, Baker received the 2008 Sackler International Prize in Biophysics.[15] Baker was elected a Fellow of the American Academy of Arts and Sciences in 2009.[16] He is married to Hannele Ruohola-Baker, another biochemist at UW. They have two college-age children.


  1. ^ http://www.bakerlab.org Baker laboratory website
  2. ^ Vincent, J. J.; Tai, C. H.; Sathyanarayana, B. K.; Lee, B. (2005). "Assessment of CASP6 predictions for new and nearly new fold targets". Proteins: Structure, Function, and Bioinformatics. 61: 67–83. doi:10.1002/prot.20722. PMID 16187347. 
  3. ^ Bradley, P.; Malmström, L.; Qian, B.; Schonbrun, J.; Chivian, D.; Kim, D. E.; Meiler, J.; Misura, K. M. S.; Baker, D. (2005). "Free modeling with Rosetta in CASP6". Proteins: Structure, Function, and Bioinformatics. 61: 128–134. doi:10.1002/prot.20729. PMID 16187354. 
  4. ^ Kuhlman, B.; Dantas, G.; Ireton, G.; Varani, G.; Stoddard, B.; Baker, D. (2003). "Design of a novel globular protein fold with atomic-level accuracy". Science. 302 (5649): 1364–1368. Bibcode:2003Sci...302.1364K. doi:10.1126/science.1089427. PMID 14631033. 
  5. ^ Gray, J.; Moughon, S.; Wang, C.; Schueler-Furman, O.; Kuhlman, B.; Rohl, C.; Baker, D. (2003). "Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations". Journal of Molecular Biology. 331 (1): 281–299. doi:10.1016/S0022-2836(03)00670-3. PMID 12875852. 
  6. ^ Bonneau, R.; Tsai, J.; Ruczinski, I.; Chivian, D.; Rohl, C.; Strauss, C. E. M.; Baker, D. (2001). "Rosetta in CASP4: Progress in ab initio protein structure prediction". Proteins: Structure, Function, and Genetics. 45: 119–126. doi:10.1002/prot.1170. PMID 11835488. 
  7. ^ Baker, D.; Hicke, L.; Rexach, M.; Schleyer, M.; Schekman, R. (1988). "Reconstitution of SEC gene product-dependent intercompartmental protein transport". Cell. 54 (3): 335–344. doi:10.1016/0092-8674(88)90196-1. PMID 3293799. 
  8. ^ Baker, D.; Wuestehube, L.; Schekman, R.; Botstein, D.; Segev, N. (1990). "GTP-binding Ypt1 protein and Ca2+ function independently in a cell-free protein transport reaction". Proceedings of the National Academy of Sciences of the United States of America. 87 (1): 355–359. Bibcode:1990PNAS...87..355B. doi:10.1073/pnas.87.1.355. PMC 53262Freely accessible. PMID 2104983. 
  9. ^ http://boinc.bakerlab.org/rosetta/ [email protected] project homepage
  10. ^ Hand, E. (2010). "Citizen science: People power". Nature. 466 (7307): 685–687. doi:10.1038/466685a. PMID 20686547. 
  11. ^ Cooper, S.; Khatib, F.; Treuille, A.; Barbero, J.; Lee, J.; Beenen, M.; Leaver-Fay, A.; Baker, D.; Popović, Z.; Players, F. (2010). "Predicting protein structures with a multiplayer online game". Nature. 466 (7307): 756–760. Bibcode:2010Natur.466..756C. doi:10.1038/nature09304. PMC 2956414Freely accessible. PMID 20686574. 
  12. ^ Dimaio, F.; Terwilliger, T. C.; Read, R. J.; Wlodawer, A.; Oberdorfer, G.; Wagner, U.; Valkov, E.; Alon, A.; Fass, D.; Axelrod, H. L.; Das, D.; Vorobiev, S. M.; Iwaï, H.; Pokkuluri, P. R.; Baker, D. (2011). "Improved molecular replacement by density- and energy-guided protein structure optimization". Nature. 473 (7348): 540. Bibcode:2011Natur.473..540D. doi:10.1038/nature09964. PMC 3365536Freely accessible. PMID 21532589. 
  13. ^ Qian, B.; Raman, S.; Das, R.; Bradley, P.; McCoy, A. J.; Read, R. J.; Baker, D. (2007). "High-resolution structure prediction and the crystallographic phase problem". Nature. 450 (7167): 259–64. Bibcode:2007Natur.450..259Q. doi:10.1038/nature06249. PMC 2504711Freely accessible. PMID 17934447. 
  14. ^ http://www.sciencemag.org/content/302/5649/1364.short
  15. ^ Leila Gray (November 24, 2008). "University of Washington biochemist David Baker to receive 2008 Sackler International Prize in Biophysics for discoveries in protein folding". University of Washington. Retrieved April 29, 2013. 
  16. ^ "Book of Members, 1780-2010: Chapter B" (PDF). American Academy of Arts and Sciences. Retrieved 5 May 2011. 

External links

  • David Baker online talk: "Crowd Sourcing Protein Folding: [email protected] and FoldIt"
  • David Baker online seminar: "Introduction to Protein Design"
  • David Baker online seminar: "Design of New Protein Functions"
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