Publications

Sort by: Author Title Type [ Year (Desc)]
2005
Chivian, D., Kim D. E., Malmström L., Schonbrun J., Rohl C. A., & Baker D. (2005).  Prediction of CASP6 structures using automated Robetta protocols. Proteins. 61 Suppl 7, 157-66. Abstract  Download: chivian05A.pdf (1.13 MB)
Morozov, A. V., Havranek J. J., Baker D., & Siggia E. D. (2005).  Protein-DNA binding specificity predictions with structural models. Nucleic acids research. 33(18), 5781-98. Abstract  Download: morozov05A.pdf (293.94 KB)
2004
Misura, K. M. S., Morozov A. V., & Baker D. (2004).  Analysis of anisotropic side-chain packing in proteins and application to high-resolution structure prediction. Journal of molecular biology. 342(2), 651-64. Abstract  Download: misura04A.pdf (867.48 KB)
Qian, B., Ortiz A. R., & Baker D. (2004).  Improvement of comparative model accuracy by free-energy optimization along principal components of natural structural variation. Proceedings of the National Academy of Sciences of the United States of America. 101(43), 15346-51. Abstract  Download: qian04A.pdf (573.21 KB)
Havranek, J. J., Duarte C. M., & Baker D. (2004).  A simple physical model for the prediction and design of protein-DNA interactions. Journal of molecular biology. 344(1), 59-70. Abstract  Download: havranek04A.pdf (445.63 KB)
Morozov, A. V., Kortemme T., Tsemekhman K., & Baker D. (2004).  Close agreement between the orientation dependence of hydrogen bonds observed in protein structures and quantum mechanical calculations. Proceedings of the National Academy of Sciences of the United States of America. 101(18), 6946-51. Abstract  Download: morozov04A.pdf (444.99 KB)
Rohl, C. A., Strauss C. E. M., Chivian D., & Baker D. (2004).  Modeling structurally variable regions in homologous proteins with rosetta. Proteins. 55(3), 656-77. Abstract  Download: rohl04A.pdf (425.56 KB)
Watters, A. L., & Baker D. (2004).  Searching for folded proteins in vitro and in silico. European journal of biochemistry. 271(9), 1615-22. Abstract  Download: watters04A.pdf (222.12 KB)
Svensson, H. G., Wedemeyer W. J., Ekstrom J. L., Callender D. R., Kortemme T., Kim D. E., et al. (2004).  Contributions of amino acid side chains to the kinetics and thermodynamics of the bivalent binding of protein L to Ig kappa light chain. Biochemistry. 43(9), 2445-57. Abstract  Download: svensson04A.pdf (522.01 KB)
Schlosshauer, M., & Baker D. (2004).  Realistic protein-protein association rates from a simple diffusional model neglecting long-range interactions, free energy barriers, and landscape ruggedness. Protein science. 13(6), 1660-9. Abstract  Download: schlosshauer04A.pdf (185.7 KB)
Kim, D. E., Chivian D., & Baker D. (2004).  Protein structure prediction and analysis using the Robetta server. Nucleic acids research. 32(Web Server issue), W526-31. Abstract  Download: kim04A.pdf (890.15 KB)
Kortemme, T., Kim D. E., & Baker D. (2004).  Computational alanine scanning of protein-protein interfaces. Science's STKE. 2004(219), pl2. Abstract  Download: kortemme04B.pdf (2.47 MB)
Kuhn, M., Meiler J., & Baker D. (2004).  Strand-loop-strand motifs: prediction of hairpins and diverging turns in proteins. Proteins. 54(2), 282-8. Abstract  Download: kuhn04A.pdf (219.88 KB)
Kortemme, T., & Baker D. (2004).  Computational design of protein-protein interactions. Current opinion in chemical biology. 8(1), 91-7. Abstract  Download: kortemme04A.pdf (204.71 KB)
Scalley-Kim, M., & Baker D. (2004).  Characterization of the folding energy landscapes of computer generated proteins suggests high folding free energy barriers and cooperativity may be consequences of natural selection. Journal of molecular biology. 338(3), 573-83. Abstract  Download: scalley-kim04A.pdf (537.27 KB)
Kortemme, T., Joachimiak L. A., Bullock A. N., Schuler A. D., Stoddard B. L., & Baker D. (2004).  Computational redesign of protein-protein interaction specificity. Nature structural & molecular biology. 11(4), 371-9. Abstract  Download: kortemme04A.pdf (1.2 MB)
Chen, Y., Kortemme T., Robertson T., Baker D., & Varani G. (2004).  A new hydrogen-bonding potential for the design of protein-RNA interactions predicts specific contacts and discriminates decoys. Nucleic acids research. 32(17), 5147-62. Abstract  Download: chen04.pdf (1.47 MB)
Rohl, C. A., Strauss C. E. M., Misura K. M. S., & Baker D. (2004).  Protein structure prediction using Rosetta.. Methods in enzymology. 383, 66-93.
AV, M., KMS M., K T., & D B. (2004).  Comparison of Quantum Mechanics and Molecular Mechanics Dimerization Energy Landscapes for Pairs of Ring-Containing Amino Acids in Proteins. Journal of Physical Chemistry B . Abstract  Download: morozov04B.pdf (287.34 KB)
2003
Dantas, G., Kuhlman B., Callender D., Wong M., & Baker D. (2003).  A large scale test of computational protein design: folding and stability of nine completely redesigned globular proteins. Journal of molecular biology. 332(2), 449-60. Abstract  Download: dantas03A.pdf (1.96 MB)
Ivankov, D. N., Garbuzynskiy S. O., Alm E., Plaxco K. W., Baker D., & Finkelstein A. V. (2003).  Contact order revisited: influence of protein size on the folding rate. Protein science. 12(9), 2057-62. Abstract  Download: ivankov03A.pdf (146.63 KB)
Boulanger, M. J., Bankovich A. J., Kortemme T., Baker D., & Garcia C. K. (2003).  Convergent mechanisms for recognition of divergent cytokines by the shared signaling receptor gp130. Molecular cell. 12(3), 577-89. Abstract  Download: boulanger03A.pdf (784.25 KB)
Meiler, J., & Baker D. (2003).  Coupled prediction of protein secondary and tertiary structure. Proceedings of the National Academy of Sciences of the United States of America. 100(21), 12105-10. Abstract  Download: meiler03A.pdf (618.84 KB)
Tsai, J., Bonneau R., Morozov A. V., Kuhlman B., Rohl C. A., & Baker D. (2003).  An improved protein decoy set for testing energy functions for protein structure prediction. Proteins. 53(1), 76-87. Abstract  Download: Tsai03A.pdf (376.65 KB)
Sadreyev, R. I., Baker D., & Grishin N. V. (2003).  Profile-profile comparisons by COMPASS predict intricate homologies between protein families. Protein science. 12(10), 2262-72. Abstract  Download: sadreyev03A.pdf (1.02 MB)
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(5649), 1364-8. Abstract  Download: kuhlman03A.pdf (2.79 MB)
Wedemeyer, W. J., & Baker D. (2003).  Efficient minimization of angle-dependent potentials for polypeptides in internal coordinates. Proteins. 53(2), 262-72. Abstract  Download: wedemeyer03A.pdf (363.38 KB)
Millet, O., Mittermaier A., Baker D., & Kay L. E. (2003).  The effects of mutations on motions of side-chains in protein L studied by 2H NMR dynamics and scalar couplings. Journal of molecular biology. 329(3), 551-63. Abstract  Download: millet03A.pdf (1.03 MB)
Gray, J. J., Moughon S. E., Kortemme T., Schueler-Furman O., Misura K. M. S., Morozov A. V., et al. (2003).  Protein-protein docking predictions for the CAPRI experiment. Proteins. 52(1), 118-22. Abstract  Download: gray03B.pdf (467.92 KB)
Kortemme, T., Morozov A. V., & Baker D. (2003).  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. Abstract  Download: kortemmea03A.pdf (2.13 MB)
Scalley-Kim, M., Minard P., & Baker D. (2003).  Low free energy cost of very long loop insertions in proteins. Protein science. 12(2), 197-206. Abstract  Download: scalley-kim03A.pdf (131.71 KB)
Meiler, J., & Baker D. (2003).  Rapid protein fold determination using unassigned NMR data. Proceedings of the National Academy of Sciences of the United States of America. 100(26), 15404-9. Abstract  Download: meiler03B.pdf (593 KB)
Hazbun, T. R., Malmström L., Anderson S., Graczyk B. J., Fox B., Riffle M., et al. (2003).  Assigning function to yeast proteins by integration of technologies. Molecular cell. 12(6), 1353-65. Abstract  Download: hazbun03A.pdf (390.65 KB)
Schueler-Furman, O., & Baker D. (2003).  Conserved residue clustering and protein structure prediction. Proteins. 52(2), 225-35. Abstract  Download: schueler-furman03A.pdf (245.13 KB)
Gray, J. J., Moughon S., Wang C., Schueler-Furman O., Kuhlman B., Rohl C. A., et al. (2003).  Protein-protein docking with simultaneous optimization of rigid-body displacement and side-chain conformations. Journal of molecular biology. 331(1), 281-99. Abstract  Download: gray03A.pdf (2.12 MB)
Yi, Q., Rajagopal P., Klevit R. E., & Baker D. (2003).  Structural and kinetic characterization of the simplified SH3 domain FP1. Protein science. 12(4), 776-83. Abstract  Download: yi03A.pdf (399.69 KB)
McFarland, B. J., Kortemme T., Yu S. F., Baker D., & Strong R. K. (2003).  Symmetry recognizing asymmetry: analysis of the interactions between the C-type lectin-like immunoreceptor NKG2D and MHC class I-like ligands. Structure. 11(4), 411-22. Abstract  Download: mcfarland03A.pdf (2.83 MB)
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)
Chivian, D., Kim D. E., Malmström L., Bradley P., Robertson T., Murphy P., et al. (2003).  Automated prediction of CASP-5 structures using the Robetta server. Proteins. 53 Suppl 6, 524-33. Abstract  Download: chivian03A.pdf (501.15 KB)
Bradley, P., Chivian D., Meiler J., Misura K. M. S., Rohl C. A., Schief W. R., et al. (2003).  Rosetta predictions in CASP5: successes, failures, and prospects for complete automation. Proteins. 53 Suppl 6, 457-68. Abstract  Download: bradley03A.pdf (1.05 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
Bonneau, R., Strauss C. E. M., Rohl C. A., Chivian D., Bradley P., Malmström L., et al. (2002).  De novo prediction of three-dimensional structures for major protein families. Journal of molecular biology. 322(1), 65-78. Abstract  Download: bonneau02B.pdf (855.42 KB)
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)
Chevalier, B. S., Kortemme T., Chadsey M. S., Baker D., Monnat R. J., & Stoddard B. L. (2002).  Design, activity, and structure of a highly specific artificial endonuclease. Molecular cell. 10(4), 895-905. Abstract  Download: chevalier02A.pdf (671.2 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
Krantz, B. A., Srivastava A. K., Nauli S., Baker D., Sauer R. T., & Sosnick T. R. (2002).  Understanding protein hydrogen bond formation with kinetic H/D amide isotope effects. Nature structural biology. 9(6), 458-63. Abstract  Download: krantz02A.pdf (2.41 MB)
Ruczinski, I., Kooperberg C., Bonneau R., & Baker D. (2002).  Distributions of beta sheets in proteins with application to structure prediction. Proteins. 48(1), 85-97. Abstract  Download: ruczinski02A.pdf (1017.65 KB)
Kuhlman, B., O'Neill J. W., Kim D. E., Zhang K. Y. J., & Baker D. (2002).  Accurate computer-based design of a new backbone conformation in the second turn of protein L. Journal of molecular biology. 315(3), 471-7. Abstract  Download: kuhlman02A.pdf (281.28 KB)
Larson, S. M., Ruczinski I., Davidson A. R., Baker D., & Plaxco K. W. (2002).  Residues participating in the protein folding nucleus do not exhibit preferential evolutionary conservation. Journal of molecular biology. 316(2), 225-33. Abstract  Download: larson02A.pdf (213.29 KB)
Nauli, S., Kuhlman B., Le Trong I., Stenkamp R. E., Teller D., & Baker D. (2002).  Crystal structures and increased stabilization of the protein G variants with switched folding pathways NuG1 and NuG2. Protein science. 11(12), 2924-31. Abstract  Download: nauli02A.pdf (257.77 KB)
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)
Schlosshauer, M., & Baker D. (2002).  Ageneral expressionforbimolecularassociationrates withorientational constraints. Physical Chemistry B.  Download: schlosshauer02A.pdf (250.05 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)
O'Neill, J. W., Kim D. E., Johnsen K., Baker D., & Zhang K. Y. (2001).  Single-site mutations induce 3D domain swapping in the B1 domain of protein L from Peptostreptococcus magnus. Structure. 9(11), 1017-27. Abstract  Download: o'neill01A.pdf (627.3 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)
Kim, K. M., Yi E. C., Baker D., & Zhang K. Y. (2001).  Post-translational modification of the N-terminal His tag interferes with the crystallization of the wild-type and mutant SH3 domains from chicken src tyrosine kinase. Acta crystallographica. Section D. 57(Pt 5), 759-62. Abstract  Download: kim01A.pdf (274.8 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)
Minard, P., Scalley-Kim M., Watters A., & Baker D. (2001).  A "loop entropy reduction" phage-display selection for folded amino acid sequences. Protein science. 10(1), 129-34. Abstract  Download: minard01A.pdf (229.21 KB)
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., Strauss C. E., & Baker D. (2001).  Improving the performance of Rosetta using multiple sequence alignment information and global measures of hydrophobic core formation. Proteins. 43(1), 1-11. Abstract  Download: bonneau01A.pdf (554.67 KB)
O'Neill, J. W., Kim D. E., Baker D., & Zhang K. Y. (2001).  Structures of the B1 domain of protein L from Peptostreptococcus magnus with a tyrosine to tryptophan substitution.. Acta crystallographica. Section D, Biological crystallography. 57(Pt 4), 480-7. 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
Bonneau, R., Tsai J., Ruczinski I., Chivian D., Rohl C., Strauss C. E., et al. (2001).  Rosetta in CASP4: progress in ab initio protein structure prediction. Proteins. Suppl 5, 119-26. Abstract  Download: bonneau01C.pdf (682.51 KB)
2000
Plaxco, K. W., Simons K. T., Ruczinski I., & Baker D. (2000).  Topology, stability, sequence, and length: defining the determinants of two-state protein folding kinetics. Biochemistry. 39(37), 11177-83. Abstract  Download: plaxco00b.pdf (70.47 KB)
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)
Bowers, P. M., Strauss C. E., & Baker D. (2000).  De novo protein structure determination using sparse NMR data.. Journal of biomolecular NMR. 18(4), 311-8. Abstract
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)