David Baker (biochemist)

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
Alma mater
Known for
Spouse(s) Hannele Ruohola-Baker
Awards
Scientific career
Fields computational biologist
Institutions
Doctoral advisor Randy Schekman
Other academic advisors David Agard
Website www.bakerlab.org

David Baker (born October 6, 1962 in Seattle, Washington) 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). He serves as the Director 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]

Life

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.

For his work on protein folding, Baker received the 2008 Sackler International Prize in Biophysics.[9] Baker was elected a Fellow of the American Academy of Arts and Sciences in 2009.[10] He is married to Hannele Ruohola-Baker, another biochemist at UW. They have two college-age children.

Professional work

Baker's group developed the Rosetta algorithm for ab initio protein structure prediction, which has been extended to a distributed computing project called Rosetta@Home[11][12] and Foldit.[13][14] The project aims to produce structural models for protein complexes as well as individual polypeptide chains. The group specializes in the CASP structure prediction experiment using ab initio methods, including both manually assisted and automated variants of the Rosetta protocol.[15][16]

Members of his group are active in the field of protein design;[17] they are noted for designing a protein, known as Top7, with an entirely novel fold.[4]

Although primarily known for development of methods for computational prediction of protein structure and function, he is also interested in the use of computational methods to drive experimental assessment of biology; his laboratory maintains an active experimental biochemistry group.

References

  1. ↑ "David Baker". Arnold and Mabel Beckman Foundation. Retrieved 1 August 2018.
  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. 1 2 Kuhlman, Brian; Dantas, Gautam; Ireton, Gregory C.; Varani, Gabriele; Stoddard, Barry L.; Baker, David (21 November 2003). "Design of a Novel Globular Protein Fold with Atomic-Level Accuracy". Science. 302 (5649): 1364–1368. doi:10.1126/science.1089427. Retrieved 2 August 2018.
  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 53262. PMID 2104983.
  9. ↑ 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.
  10. ↑ "Book of Members, 1780-2010: Chapter B" (PDF). American Academy of Arts and Sciences. Retrieved 5 May 2011.
  11. ↑ Castillo, Oscar; Melin, Patricia; Kacprzyk, Janusz, eds. (2018). Fuzzy Logic Augmentation of Neural and Optimization Algorithms: Theoretical Aspects and Real Applications. Springer. p. 455. ISBN 9783319710075. Retrieved 2 August 2018.
  12. ↑ Bonneau, Richard; Ruczinski, Ingo; Tsai, Jerry; Baker, David (August 2002). "Contact order and ab initio protein structure prediction". Protein Science. 11 (8): 1937–1944. doi:10.1110/ps.3790102. PMC 2373674. PMID 12142448.
  13. ↑ Hand, E. (2010). "Citizen science: People power". Nature. 466 (7307): 685–687. doi:10.1038/466685a. PMID 20686547.
  14. ↑ 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 2956414. PMID 20686574.
  15. ↑ 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 3365536. PMID 21532589.
  16. ↑ 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 2504711. PMID 17934447.
  17. ↑ Zimmer, Carl (December 26, 2017). "Scientists Are Designing Artisanal Proteins for Your Body". The New York Times. Retrieved 2 August 2018.
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