Dr. David Baker

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University of Washington
School of Medicine
Biochemistry
Associate ProfessorAppointed: 1998
Howard Hughes Medical Institute
Associate Investigator

Mailing Address

Box 357350
University of Washington
Seattle, Washington 98195
United States

Contact Information

Phone: (206) 543-1295
Fax: (206) 685-1792
dabaker@u.washington.edu
depts.washington.edu/bakerpg/

Qualifications

Ph.D., University of California, Berkeley, Biochemistry, 1989.
B.A., Harvard University, 1984.
Postdoctoral Research 1990-93, University of California, San Francisco, Biophysics.

Expertise and Research Interests

Our research is focused on the prediction and design of protein structures, protein folding mechanisms, and protein protein 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. A particularly exciting recent success with this approach was the development of the ROSETTA method for ab initio protein structure prediction, which produced de novo structure predictions of unprecedented accuraccy in the recent CASP4 international blind test of protein structure prediction methods. We are currently working to appply these methods to the interpretation of genome sequence information.

Keywords

COS Keywords:

Biochemistry, Biophysical Interactions, Computer Technology (medical), Molecular Biology, Protein Structure.

Additional Terms:

Molecular Structure.

Honors and Awards

Overton award, ISMB
Packard Fellowship in Science and Engineering, Packard Foundation
Young Investigator Award, National Science Foundation
Young Investigator Award, Beckman Foundation
Young Investigator Award, Protein Society

Publications

  • Schueler-Furman O, Baker D, Conserved residue clustering and protein structure prediction, Proteins, 52(2), 225-35, August 2003 Abstract
  • Gray JJ, Moughon S, Wang C, Schueler-Furman O, Kuhlman B, Rohl CA, Baker D, Protein-Protein Docking with Simultaneous Optimization of Rigid-body Displacement and Side-chain Conformations, Journal of Molecular Biology, 331(1), 281-99, August 2003 Abstract
  • Gray JJ, Moughon SE, Kortemme T, Schueler-Furman O, Misura KM, Morozov AV, Baker D, Protein-protein docking predictions for the CAPRI experiment, Proteins, 52(1), 118-22, July 2003 Abstract
  • Yi Q, Rajagopal P, Klevit RE, Baker D, Structural and kinetic characterization of the simplified SH3 domain FP1, Protein Science : a Publication of the Protein Society, 12(4), 776-83, April 2003 Abstract
  • Kortemme T, Morozov AV, Baker D, An orientation-dependent hydrogen bonding potential improves prediction of specificity and structure for proteins and protein-protein complexes, Journal of Molecular Biology, 326(4), 1239-59, February 2003 Abstract
  • Scalley-Kim M, Minard P, Baker D, Low free energy cost of very long loop insertions in proteins, Protein Science : a Publication of the Protein Society, 12(2), 197-206, February 2003 Abstract
  • Chivian D, Robertson T, Bonneau R, Baker D, Ab initio methods, Methods of Biochemical Analysis, 44, 547-57, 2003 Abstract
  • Alm E, Morozov A, Kortemme T, Baker D., Simple physical models connect theory and experiment in protein folding kinetics, Journal of Molecular Biology, 322(2), 463, 13 Sep 2002
  • Saunders C, Baker D, Evaluation of structural and evolutionary contributions to deleterious mutation prediction, Journal of Molecular Biology, 322(4), 891, September 2002 Abstract
  • Bonneau R, Strauss C, Rohl C, Chivian D, Bradley P, Malmstrom L, Robertson T, Baker D, De Novo Prediction of Three-dimensional Structures for Major Protein Families, Journal of Molecular Biology, 322(1), 65, September 2002 Abstract
  • Bonneau R, Ruczinski I, Tsai J, Baker D, Contact order and ab initio protein structure prediction, Protein Science : a Publication of the Protein Society, 11(8), 1937-44, Aug 2002 Abstract
  • Ruczinski I, Kooperberg C, Bonneau R, Baker D, Distributions of beta sheets in proteins with application to structure prediction, Proteins, 48(1), 85-97, July 2002 Abstract
  • Schonbrun J, Wedemeyer WJ, Baker D, Protein structure prediction in 2002, Current Opinion in Structural Biology, 12(3), 348-54, June 2002
  • Schonbrun J, Wedemeyer WJ, Baker D, Protein structure prediction in 2002, Current Opinion in Structural Biology, 12(3), 348-54, June 2002 Abstract
  • Rohl CA, Baker D, De novo determination of protein backbone structure from residual dipolar couplings using Rosetta, Journal of the American Chemical Society, 124(11), 2723-9, March 2002 Abstract
  • Baker D, Lim WA, From folding towards function, 12(1), 11-3, February 2002
  • Kuhlman B, O'Neill JW, Kim DE, Zhang KY, Baker D, Accurate computer-based design of a new backbone conformation in the second turn of protein L, Journal of Molecular Biology, 315(3), 471-7, January 2002 Abstract
  • Baker D, Sali A, Protein structure prediction and structural genomics, Science, 294(5540), 93-6, 2001 Abstract
  • Kuhlman B, O'Neill JW, Kim DE, Zhang KY, Baker D, Conversion of monomeric protein L to an obligate dimer by computational protein design, Proceedings of the National Academy of Sciences (USA), 98(19), 10687-91, 2001 Abstract
  • Nauli S, Kuhlman B, Baker D, Computer-based redesign of a protein folding pathway, Nature Structural Biology, 8(7), 602-5, July 2001 Abstract
  • Bonneau R, Strauss CE, Baker D, Improving the performance of Rosetta using multiple sequence alignment information and global measures of hydrophobic core formation, Proteins, 43(1), 1-11, 2001 Abstract
  • Simons KT, Strauss C, Baker D, Prospects for ab initio protein structural genomics, Journal of Molecular Biology, 306(5), 1191-9, 2001 Abstract
  • Grantcharova VP, Baker D, Circularization changes the folding transition state of the src SH3 domain, Journal of Molecular Biology, 306(3), 555-63, 2001 Abstract
  • Grantcharova V, Alm EJ, Baker D, Horwich AL, Mechanisms of protein folding, Current Opinion in Structural Biology, 11(1), 70-82, February 2001 Abstract
  • Bonneau R, Baker D, Ab initio protein structure prediction: progress and prospects, Annual Review of Biophysics and Biomolecular Structure, 30, 173-89, 2001 Abstract
  • Minard P, Scalley-Kim M, Watters A, Baker D, A 'loop entropy reduction' phage-display selection for folded amino acid sequences, Protein Science, 10(1), 129-34, Jan 2001 Abstract
  • Bowers PM, Strauss CE, Baker D, De novo protein structure determination using sparse NMR data, Journal of Biomolecular Nmr, 18(4), 311-8, December 2000 Abstract
  • Plaxco KW, Simons KT, Ruczinski I, Baker D, Topology, stability, sequence, and length: defining the determinants of two-state protein folding kinetics, Biochemistry, 39(37), 11177-83, 2000 Abstract
  • Kuhlman B, Baker D, Native protein sequences are close to optimal for their structures, Proceedings of the National Academy of Sciences (USA), 97(19), 10383-8, 2000 Abstract
  • Bystroff C, Thorsson V, Baker D, HMMSTR: a hidden Markov model for local sequence-structure correlations in proteins, Journal of Molecular Biology, 301(1), 173-90, 2000 Abstract
  • McCallister EL, Alm E, Baker D, Critical role of beta-hairpin formation in protein G folding, Nature Structural Biology, 7(8), 669-73, August 2000 Abstract
  • Yi Q, Scalley-Kim ML, Alm EJ, Baker D, NMR characterization of residual structure in the denatured state of protein L, Journal of Molecular Biology, 299(5), 1341-51, 2000 Abstract
  • Grantcharova VP, Riddle DS, Baker D, Long-range order in the src SH3 folding transition state, Proceedings of the National Academy of Sciences (USA), 97(13), 7084-9, 2000 Abstract
  • Kim DE, Fisher C, Baker D, A breakdown of symmetry in the folding transition state of protein L, Journal of Molecular Biology, 298(5), 971-84, 2000 Abstract
  • Baker D, A surprising simplicity to protein folding, Nature, 405(6782), 39-42, 2000 Abstract
  • Plaxco KW, Larson S, Ruczinski I, Riddle DS, Thayer EC, Buchwitz B, Davidson AR, Baker D, Evolutionary conservation in protein folding kinetics, Journal of Molecular Biology, 298(2), 303-12, 2000 Abstract
  • Gu H, Doshi N, Kim DE, Simons KT, Santiago JV, Nauli S, Baker D, Robustness of protein folding kinetics to surface hydrophobic substitutions, Protein Science, 8(12), 2734-41, December 1999 Abstract
  • Scalley ML, Nauli S, Gladwin ST, Baker D, Structural transitions in the protein L denatured state ensemble, Biochemistry, 38(48), 15927-35, 1999 Abstract
  • Riddle DS, Grantcharova VP, Santiago JV, Alm E, Ruczinski I, Baker D., Experiment and theory highlight role of native state topology in SH3 folding, Nature Structural Biology, 6(11), 987-90, 6 Nov 1999
  • Alm E, Baker D, Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures, Proceedings of the National Academy of Sciences (USA), 96(20), 11305-10, 1999 Abstract
  • Tsai J, Levitt M, Baker D, Hierarchy of structure loss in MD simulations of src SH3 domain unfolding, Journal of Molecular Biology, 291(1), 215-25, 1999 Abstract
  • Plaxco KW, Millett IS, Segel DJ, Doniach S, Baker D, Chain collapse can occur concomitantly with the rate-limiting step in protein folding, Nature Structural Biology, 6(6), 554-6, June 1999 Abstract
  • Alm E, Baker D, Matching theory and experiment in protein folding, Current Opinion in Structural Biology, 9(2), 189-96, April 1999 Abstract
  • Simons KT, Bonneau R, Ruczinski I, Baker D, Ab initio protein structure prediction of CASP III targets using ROSETTA, Proteins, Suppl 3, 171-6, 1999 Abstract
  • Simons KT, Ruczinski I, Kooperberg C, Fox BA, Bystroff C, Baker D, Improved recognition of native-like protein structures using a combination of sequence-dependent and sequence-independent features of proteins, Proteins, 34(1), 82-95, 1999 Abstract
  • Kim DE, Yi Q, Gladwin ST, Goldberg JM, Baker D, The single helix in protein L is largely disrupted at the rate-limiting step in folding, Journal of Molecular Biology, 284(3), 807-15, 1998 Abstract
  • Baker D, Metastable states and folding free energy barriers, Nature Structural Biology, 5(12), 1021-4, December 1998 Abstract
  • Plaxco KW, Baker D, Limited internal friction in the rate-limiting step of a two-state protein folding reaction, Proceedings of the National Academy of Sciences (USA), 95(23), 13591-6, 1998 Abstract
  • Bystroff C, Baker D, Prediction of local structure in proteins using a library of sequence-structure motifs, Journal of Molecular Biology, 281(3), 565-77, 1998 Abstract
  • Grantcharova VP, Riddle DS, Santiago JV, Baker D, Important role of hydrogen bonds in the structurally polarized transition state for folding of the src SH3 domain, Nature Structural Biology, 5(8), 714-20, August 1998 Abstract
  • Rank JA, Baker D, Contributions of solvent-solvent hydrogen bonding and van der Waals interactions to the attraction between methane molecules in water, Biophysical Chemistry, 71(2-3), 199-204, 1998 Abstract
  • Plaxco, K. W., Riddle, D. S., Grantcharova, V. and Baker, D., Simplified proteins: minimalist solutions to the 'protein folding problem', Current Opinion in Structural Biology, 8, 80, 1998
  • Plaxco, K. W., Simons, K. T., and Baker, D., Contact order, transition state placement, and the refolding rates of single domain proteins, Journal of Molecular Biology, 277, 985, 1998
  • Kim, D. E., Gu, H., and Baker, D., The sequences of small proteins are not extensively optimized for rapid folding by natural selection, Proceedings of the National Academy of Sciences, 95, 4982, 1998
  • Shortle, D., Simons, K. T. and Baker, D., Clustering of low energy conformations near the native structures of small proteins, Proceedings of the National Academy of Sciences, 95, 11158, 1998
  • Bystroff, C. and Baker, D., Local structure prediction using a library of sequence-structure motifs, Journal of Molecular Biology, 281, 565, 1998
  • Yi, Q., Bystroff, C., Rajagopal, P., Klevit, R. E. and Baker, D., Prediction and structural characterization of an independently folding substructure in the src SH3 domain, Journal of Molecular Biology, 283, 293, 1998
  • Plaxco, K. W. and Baker, D., Limited internal friction in the rate-limiting step of a two-state protein folding reaction, Proceedings of the National Academy of Sciences, 1998
  • A desolvation barrier to hydrophobic cluster formation may contribute to the rate limiting step in protein folding, Rank, J. and Baker, D., 6, 347, 1997
  • Han, K. F., Bystroff, C. and Baker, D., Three-dimensional structures and contexts associated with recurrent amino acid sequence patterns, Protein Science, 6, 1587, 1997
  • Scalley, M. L., Yi, Q., Gu, H., McCormack, A., Yates, J. R., and Baker, D., Kinetics of folding of the IgG binding domain of peptostreptoccocal protein L, Biochemistry, 36, 3373 abstract, 1997
  • Simons, K. T., Kooperberg, C., Huang, E. and Baker, D., Assembly of protein tertiary structures from fragments with similar local sequences using simulated anealing and Bayesian scoring functions, Journal of Molecular Biology, 268, 209 abstract, 1997
  • Doyle, R., Simons, K., Qian, H., and Baker, D., Local interactions and the optimization of protein folding, Proteins, 29, 282, 1997
  • Riddle, D., Santiago, J., Grantcharova, V. and Baker, D., Functional rapidly folding proteins from simplified amino acid sequences, Nature Structural Biology, 4, 805, 1997
  • Gu, H., Kim, D.E. and Baker, D., Contrasting roles for symmetrically disposed beta turns in the folding of a small protein, Journal of Molecular Biology, 274, 588, 1997
  • Scalley, M. and Baker, D., Protein folding kinetics exhibit an Arrhenius temperature dependence when corrected for the temperature dependence of protein stability, Proceedings of the National Academy of Sciences, 94, 10636, 1997
  • Grantcharova, V. and Baker, D., Folding dynamics of the Src SH3 domain, Biochemistry, 36, 15685, 1997
  • Yi, Q., Scalley, M., Simons, K and Baker, D., Characterization of the free energy spectrum of Peptostreptococcal protein L, Folding and Design, 2, 271, 1997
  • Bystroff, C. and Baker, D., Blind predictions of local protein structure in the CASP2 targets using the ISITES library, Proteins, Suppl 1, 167, 1997
  • Bystroff C, Simons KT, Han KF, Baker D, Local sequence-structure correlations in proteins, Current Opinion in Biotechnology, 7(4), 417-21, August 1996 Abstract
  • Han KF, Baker D, Global properties of the mapping between local amino acid sequence and local structure in proteins, Proceedings of the National Academy of Sciences (USA), 93(12), 5814-8, June 1996 Abstract
  • Yi, Q. and Baker D., Direct evidence for a two-state protein unfolding transition from hydrogen-deuterium exchange, mass spectrometry, and NMR, Protein Science, 5, 1060, 1996
  • Han KF, Baker D, Recurring local sequence motifs in proteins, Journal of Molecular Biology, 251(1), 176-87, August 1995 Abstract
  • Gu H, Yi Q, Bray ST, Riddle DS, Shiau AK, Baker D, A phage display system for studying the sequence determinants of protein folding, Protein Science : a Publication of the Protein Society, 4(6), 1108-17, June 1995 Abstract
  • Baker D, Shiau AK, Agard DA, The role of pro regions in protein folding, Current Opinion in Cell Biology, 5(6), 966-70, December 1993 Abstract
  • Baker D, Silen JL, Agard DA, Protease pro region required for folding is a potent inhibitor of the mature enzyme, Proteins, 12(4), 339-44, April 1992 Abstract
  • Baker D, Sohl JL, Agard DA, A protein-folding reaction under kinetic control, Nature, 356(6366), 263-5, March 1992 Abstract

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Last Updated: 8/7/2003

COS Expertise ID #307283
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