Publications

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2002
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)
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)
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)
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)
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)
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)
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)
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)
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)
2003
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
2004
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)
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.
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)
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., & 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)
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., 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)
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)
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)
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)
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)
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)
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)
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)
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)
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)
2005
Kim, D. E., Chivian D., Malmström L., & Baker D. (2005).  Automated prediction of domain boundaries in CASP6 targets using Ginzu and RosettaDOM. Proteins. 61 Suppl 7, 193-200. Abstract  Download: kim05A.pdf (683.21 KB)
Graña, O., Baker D., MacCallum R. M., Meiler J., Punta M., Rost B., et al. (2005).  CASP6 assessment of contact prediction. Proteins. 61 Suppl 7, 214-24. Abstract  Download: grana05A.pdf (857.44 KB)
Bradley, P., Malmström L., Qian B., Schonbrun J., Chivian D., Kim D. E., et al. (2005).  Free modeling with Rosetta in CASP6. Proteins. 61 Suppl 7, 128-34. Abstract  Download: bradley05A.pdf (1.17 MB)
Cheng, G., Qian B., Samudrala R., & Baker D. (2005).  Improvement in protein functional site prediction by distinguishing structural and functional constraints on protein family evolution using computational design. Nucleic acids research. 33(18), 5861-7. Abstract  Download: cheng05A.pdf (507.13 KB)
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)
Meiler, J., & Baker D. (2005).  The fumarate sensor DcuS: progress in rapid protein fold elucidation by combining protein structure prediction methods with NMR spectroscopy. Journal of magnetic resonance. 173(2), 310-6. Abstract  Download: meiler05A.pdf (657.1 KB)
Misura, K. M. S., & Baker D. (2005).  Progress and challenges in high-resolution refinement of protein structure models. Proteins. 59(1), 15-29. Abstract  Download: misura05A.pdf (651.28 KB)
Schueler-Furman, O., Wang C., & Baker D. (2005).  Progress in protein-protein docking: atomic resolution predictions in the CAPRI experiment using RosettaDock with an improved treatment of side-chain flexibility. Proteins. 60(2), 187-94. Abstract  Download: schueler-rurman05A.pdf (333.32 KB)
Saunders, C. T., & Baker D. (2005).  Recapitulation of protein family divergence using flexible backbone protein design. Journal of molecular biology. 346(2), 631-44. Abstract  Download: saundersa05A.pdf (639.35 KB)
Jiang, L., Kuhlman B., Kortemme T., & Baker D. (2005).  A "solvated rotamer" approach to modeling water-mediated hydrogen bonds at protein-protein interfaces. Proteins. 58(4), 893-904. Abstract  Download: jiang05A.pdf (723.29 KB)
Wang, C., Schueler-Furman O., & Baker D. (2005).  Improved side-chain modeling for protein-protein docking. Protein science. 14(5), 1328-39. Abstract  Download: wang05A.pdf (736.4 KB)
Korkegian, A., Black M. E., Baker D., & Stoddard B. L. (2005).  Computational thermostabilization of an enzyme. Science. 308(5723), 857-60. Abstract  Download: korkegian05A.pdf (274.59 KB)
Lacy, B. D., Lin H. C., Melnyk R. A., Schueler-Furman O., Reither L., Cunningham K., et al. (2005).  A model of anthrax toxin lethal factor bound to protective antigen. Proceedings of the National Academy of Sciences of the United States of America. 102(45), 16409-14. Abstract  Download: lacy05A.pdf (621.23 KB)
Schueler-Furman, O., Wang C., Bradley P., Misura K., & Baker D. (2005).  Progress in modeling of protein structures and interactions. Science. 310(5748), 638-42. Abstract  Download: schueler-furman05B.pdf (313.68 KB)
Bradley, P., Misura K. M. S., & Baker D. (2005).  Toward high-resolution de novo structure prediction for small proteins. Science. 309(5742), 1868-71. Abstract  Download: bradley05B.pdf (421.25 KB)
2006
Chivian, D., & Baker D. (2006).  Homology modeling using parametric alignment ensemble generation with consensus and energy-based model selection. Nucleic acids research. 34(17), e112. Abstract  Download: chivian06A.pdf (1.95 MB)
Misura, K. M. S., Chivian D., Rohl C. A., Kim D. E., & Baker D. (2006).  Physically realistic homology models built with ROSETTA can be more accurate than their templates. Proceedings of the National Academy of Sciences of the United States of America. 103(14), 5361-6. Abstract  Download: misura06A.pdf (2.12 MB)
Joachimiak, L. A., Kortemme T., Stoddard B. L., & Baker D. (2006).  Computational design of a new hydrogen bond network and at least a 300-fold specificity switch at a protein-protein interface. Journal of molecular biology. 361(1), 195-208. Abstract  Download: joachimiak06A.pdf (1.04 MB)
Zanghellini, A., Jiang L., Wollacott A. M., Cheng G., Meiler J., Althoff E. A., et al. (2006).  New algorithms and an in silico benchmark for computational enzyme design. Protein science : a publication of the Protein Society. 15(12), 2785-94. Abstract  Download: zanghellini06A.pdf (497.12 KB)
Bradley, P., & Baker D. (2006).  Improved beta-protein structure prediction by multilevel optimization of nonlocal strand pairings and local backbone conformation. Proteins. 65(4), 922-9. Abstract  Download: bradley06A.pdf (837.59 KB)
Song, G., Lazar G. A., Kortemme T., Shimaoka M., Desjarlais J. R., Baker D., et al. (2006).  Rational design of intercellular adhesion molecule-1 (ICAM-1) variants for antagonizing integrin lymphocyte function-associated antigen-1-dependent adhesion. The Journal of biological chemistry. 281(8), 5042-9. Abstract  Download: song06A.pdf (277.35 KB)
Sprague, E. R., Wang C., Baker D., & Bjorkman P. J. (2006).  Crystal structure of the HSV-1 Fc receptor bound to Fc reveals a mechanism for antibody bipolar bridging. PLoS biology. 4(6), e148. Abstract  Download: sprague06A.pdf (539.35 KB)
Ashworth, J., Havranek J. J., Duarte C. M., Sussman D., Monnat R. J., Stoddard B. L., et al. (2006).  Computational redesign of endonuclease DNA binding and cleavage specificity. Nature. 441(7093), 656-9. Abstract  Download: ashworth06A.pdf (664.23 KB)
Yarov-Yarovoy, V., Schonbrun J., & Baker D. (2006).  Multipass membrane protein structure prediction using Rosetta. Proteins. 62(4), 1010-25. Abstract  Download: yarov-yarovoy06B.pdf (1.31 MB)
Thompson, M. J., Sievers S. A., Karanicolas J., Ivanova M. I., Baker D., & Eisenberg D. (2006).  The 3D profile method for identifying fibril-forming segments of proteins. Proceedings of the National Academy of Sciences of the United States of America. 103(11), 4074-8. Abstract  Download: thompson06A.pdf (738.97 KB)
Morozov, A. V., Tsemekhman K., & Baker D. (2006).  Electron density redistribution accounts for half the cooperativity of alpha helix formation. The journal of physical chemistry. B. 110(10), 4503-5. Abstract  Download: morozov06A.pdf (132.16 KB)
Baker, D. (2006).  Prediction and design of macromolecular structures and interactions. Philosophical transactions of the Royal Society of London. 361(1467), 459-63. Abstract  Download: baker06A.pdf (688.82 KB)
Sood, V. D., & Baker D. (2006).  Recapitulation and design of protein binding peptide structures and sequences. Journal of molecular biology. 357(3), 917-27. Abstract  Download: sood06A.pdf (497.29 KB)
Palmer, A. E., Giacomello M., Kortemme T., Hires A. S., Lev-Ram V., Baker D., et al. (2006).  Ca2+ indicators based on computationally redesigned calmodulin-peptide pairs. Chemistry & biology. 13(5), 521-30. Abstract  Download: palmer06A.pdf (591.03 KB)
Dobson, N., Dantas G., Baker D., & Varani G. (2006).  High-resolution structural validation of the computational redesign of human U1A protein. Structure. 14(5), 847-56. Abstract  Download: dobson06A.pdf (448.74 KB)