Publications

Found 338 results

2003
Chivian, D., Robertson T., Bonneau R., & Baker D. (2003).  Ab initio methods. Methods of biochemical analysis. 44, 547-57. Download: chivan03A.pdf (5.89 MB)
Morozov, A., Kortemme T., & Baker D. (2003).  Evaluation of Models of Electrostatic Interactions in Proteins. Journal of Physical Chemistry B. 107(9), 2075-2090. Abstract  Download: morozov03A.pdf (691.51 KB)
2002
Saunders, C. T., & Baker D. (2002).  Evaluation of structural and evolutionary contributions to deleterious mutation prediction. Journal of molecular biology. 322(4), 891-901. Abstract  Download: saunders02A.pdf (484.42 KB)
Alm, E., Morozov A. V., Kortemme T., & Baker D. (2002).  Simple physical models connect theory and experiment in protein folding kinetics. Journal of molecular biology. 322(2), 463-76. Abstract  Download: alm02A.pdf (1.2 MB)
Kortemme, T., & Baker D. (2002).  A simple physical model for binding energy hot spots in protein-protein complexes. Proceedings of the National Academy of Sciences of the United States of America. 99(22), 14116-21. Abstract  Download: kortemme02A.pdf (200.71 KB)
Rohl, C. A., & Baker D. (2002).  De novo determination of protein backbone structure from residual dipolar couplings using Rosetta. Journal of the American Chemical Society. 124(11), 2723-9. Abstract  Download: rohl02A.pdf (265.13 KB)
Schonbrun, J., Wedemeyer W. J., & Baker D. (2002).  Protein structure prediction in 2002.. Current opinion in structural biology. 12(3), 348-54. Abstract
Bonneau, R., Ruczinski I., Tsai J., & Baker D. (2002).  Contact order and ab initio protein structure prediction. Protein science. 11(8), 1937-44. Abstract  Download: bonneau02A.pdf (259.2 KB)
2001
Kuhlman, B., O'Neill J. W., Kim D. E., Zhang K. Y., & Baker D. (2001).  Conversion of monomeric protein L to an obligate dimer by computational protein design. Proceedings of the National Academy of Sciences of the United States of America. 98(19), 10687-91. Abstract  Download: kuhlman01A.pdf (558.98 KB)
Baker, D., & Sali A. (2001).  Protein structure prediction and structural genomics.. Science (New York, N.Y.). 294(5540), 93-6. Abstract
Lee, M. R., Tsai J., Baker D., & Kollman P. A. (2001).  Molecular dynamics in the endgame of protein structure prediction. Journal of molecular biology. 313(2), 417-30. Abstract  Download: lee01B.pdf (814.49 KB)
Bonneau, R., Tsai J., Ruczinski I., & Baker D. (2001).  Functional inferences from blind ab initio protein structure predictions. Journal of structural biology. 134(2-3), 186-90. Abstract  Download: bonneau01B.pdf (115.55 KB)
Simons, K. T., Strauss C., & Baker D. (2001).  Prospects for ab initio protein structural genomics. Journal of molecular biology. 306(5), 1191-9. Abstract  Download: simons01A.pdf (282.77 KB)
Nauli, S., Kuhlman B., & Baker D. (2001).  Computer-based redesign of a protein folding pathway.. Nature structural biology. 8(7), 602-5. Abstract  Download: nauli01A.pdf (1.39 MB)
Grantcharova, V. P., & Baker D. (2001).  Circularization changes the folding transition state of the src SH3 domain. Journal of molecular biology. 306(3), 555-63. Abstract  Download: grantcharova01A.pdf (341.23 KB)
Lee, M. R., Baker D., & Kollman P. A. (2001).  2.1 and 1.8 A average C(alpha) RMSD structure predictions on two small proteins, HP-36 and s15. Journal of the American Chemical Society. 123(6), 1040-6. Abstract  Download: lee01A.pdf (180.46 KB)
Grantcharova, V., Alm E. J., Baker D., & Horwich A. L. (2001).  Mechanisms of protein folding.. Current opinion in structural biology. 11(1), 70-82. Abstract
Bonneau, R., & Baker D. (2001).  Ab initio protein structure prediction: progress and prospects.. Annual review of biophysics and biomolecular structure. 30, 173-89. Abstract
2000
Kuhlman, B., & Baker D. (2000).  Native protein sequences are close to optimal for their structures. Proceedings of the National Academy of Sciences of the United States of America. 97(19), 10383-8. Abstract  Download: kuhlman00A.pdf (142.94 KB)
Baker, D. (2000).  A surprising simplicity to protein folding. Nature. 405(6782), 39-42. Abstract  Download: baker00A.pdf (853.11 KB)
Kim, D. E., Fisher C., & Baker D. (2000).  A breakdown of symmetry in the folding transition state of protein L. Journal of molecular biology. 298(5), 971-84. Abstract  Download: kim00A.pdf (416.01 KB)
Yi, Q., Scalley-Kim M. L., Alm E. J., & Baker D. (2000).  NMR characterization of residual structure in the denatured state of protein L. Journal of molecular biology. 299(5), 1341-51. Abstract  Download: yia00A.pdf (309.07 KB)
Grantcharova, V. P., Riddle D. S., & Baker D. (2000).  Long-range order in the src SH3 folding transition state. Proceedings of the National Academy of Sciences of the United States of America. 97(13), 7084-9. Abstract  Download: grantcharova00A.pdf (313 KB)
Thayer, E. C., Bystroff C., & Baker D. (2000).  Detection of protein coding sequences using a mixture model for local protein amino acid sequence. Journal of computational biology : a journal of computational molecular cell biology. 7(1-2), 317-27. Abstract  Download: thayer00A.pdf (244.63 KB)
Bystroff, C., Thorsson V., & Baker D. (2000).  HMMSTR: a hidden Markov model for local sequence-structure correlations in proteins. Journal of molecular biology. 301(1), 173-90. Abstract  Download: bystroff00A.pdf (730.85 KB)
McCallister, E. L., Alm E., & Baker D. (2000).  Critical role of beta-hairpin formation in protein G folding. Nature structural biology. 7(8), 669-73. Abstract  Download: mccallister00A.pdf (785.9 KB)
Plaxco, K. W., Larson S., Ruczinski I., Riddle D. S., Thayer E. C., Buchwitz B., et al. (2000).  Evolutionary conservation in protein folding kinetics. Journal of molecular biology. 298(2), 303-12. Abstract  Download: plaxco00a.pdf (214.04 KB)
1999
Alm, E., & Baker D. (1999).  Prediction of protein-folding mechanisms from free-energy landscapes derived from native structures. Proceedings of the National Academy of Sciences of the United States of America. 96(20), 11305-10. Abstract  Download: alm99A.pdf (574.66 KB)
Tsai, J., Levitt M., & Baker D. (1999).  Hierarchy of structure loss in MD simulations of src SH3 domain unfolding. Journal of molecular biology. 291(1), 215-25. Abstract  Download: tsai99A.pdf (666.2 KB)
Baker, D., & DeGrado W. F. (1999).  Engineering and design. Current opinion in structural biology. 9(4), 485-6.
Alm, E., & Baker D. (1999).  Matching theory and experiment in protein folding.. Current opinion in structural biology. 9(2), 189-96. Abstract
1998
Shortle, D., Simons K. T., & Baker D. (1998).  Clustering of low-energy conformations near the native structures of small proteins. Proceedings of the National Academy of Sciences of the United States of America. 95(19), 11158-62. Abstract  Download: shortle98A.pdf (243.13 KB)
Plaxco, K. W., & Baker D. (1998).  Limited internal friction in the rate-limiting step of a two-state protein folding reaction. Proceedings of the National Academy of Sciences of the United States of America. 95(23), 13591-6. Abstract  Download: plaxco98A.pdf (205 KB)
Baker, D. (1998).  Metastable states and folding free energy barriers.. Nature structural biology. 5(12), 1021-4.
Bystroff, C., & Baker D. (1998).  Prediction of local structure in proteins using a library of sequence-structure motifs. Journal of molecular biology. 281(3), 565-77. Abstract  Download: bystroff98A.pdf (1.76 MB)
Kim, D. E., Gu H., & Baker D. (1998).  The sequences of small proteins are not extensively optimized for rapid folding by natural selection. Proceedings of the National Academy of Sciences of the United States of America. 95(9), 4982-6. Abstract  Download: kim98A.pdf (220.84 KB)
1997
Scalley, M. L., & Baker D. (1997).  Protein folding kinetics exhibit an Arrhenius temperature dependence when corrected for the temperature dependence of protein stability. Proceedings of the National Academy of Sciences of the United States of America. 94(20), 10636-40. Abstract  Download: scalley97A.pdf (249.15 KB)
Doyle, R., Simons K., Qian H., & Baker D. (1997).  Local interactions and the optimization of protein folding. Proteins. 29(3), 282-91. Abstract  Download: doyle97A.pdf (161.67 KB)
Grantcharova, V. P., & Baker D. (1997).  Folding dynamics of the src SH3 domain. Biochemistry. 36(50), 15685-92. Abstract  Download: grantcharova97A.pdf (171.64 KB)
Gu, H., Kim D. E., & Baker D. (1997).  Contrasting roles for symmetrically disposed beta-turns in the folding of a small protein. Journal of molecular biology. 274(4), 588-96. Abstract  Download: gu97A.pdf (654.1 KB)