David Baker (biochemist)

David Baker is an American biochemist and computational biologist who studies methods to predict the three-dimensional structures of proteins. He is a faculty member in the Department of Biochemistry at the University of Washington in Seattle, Washington.

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The Baker laboratory developed the Rosetta algorithm for ab initio protein structure prediction, which has been extended to a distributed computing project called Rosetta@Home. 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.

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.

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. Although now known best for their computational work, the Baker laboratory currently maintains an active experimental biochemistry group.

References

Computational work

• Bradley, P., Malmstrom, L., Qian, B., Schonbrun, J., Chivian, D., Kim, D. E., Meiler, J., Misura, K. M., Baker, D. (2005). Free modeling with Rosetta in CASP6. Proteins 61 Suppl 7:128-34.
• Kuhlman, B., Dantas, G., Ireton, G. C., Varani, G., Stoddard, B. L., Baker, D. (2003). Design of a novel globular protein fold with atomic-level accuracy Science 302, 1364-8.
• Vincent JJ, Tai CH, Sathyanarayana BK, Lee B. (2005). Assessment of CASP6 predictions for new and nearly new fold targets. Proteins 61 Suppl 7:67-83.

Yeast work

• Baker D, Hicke L, Rexach M, Schleyer M, Schekman R. (1988). Reconstitution of SEC gene product-dependent intercompartmental protein transport. Cell 54(3):335-44.
• 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. Proc Natl Acad Sci 87(1):355-9.