Publications

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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)
Wang, C., Bradley P., & Baker D. (2007).  Protein-protein docking with backbone flexibility. Journal of molecular biology. 373(2), 503-19. Abstract  Download: wang07A.pdf (1.57 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)
Baker, D., Sohl J. L., & Agard D. A. (1992).  A protein-folding reaction under kinetic control. Nature. 356(6366), 263-5. Abstract  Download: baker92A.pdf (384.94 KB)
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)
Payne, G. S., Baker D., van Tuinen E., & Schekman R. (1988).  Protein transport to the vacuole and receptor-mediated endocytosis by clathrin heavy chain-deficient yeast. The Journal of cell biology. 106(5), 1453-61. Abstract  Download: payne88A.pdf (2.11 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.
Schonbrun, J., Wedemeyer W. J., & Baker D. (2002).  Protein structure prediction in 2002.. Current opinion in structural biology. 12(3), 348-54. Abstract
Baker, D., & Sali A. (2001).  Protein structure prediction and structural genomics.. Science (New York, N.Y.). 294(5540), 93-6. Abstract
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)
Schmitz, C., Vernon R., Otting G., Baker D., & Huber T. (2012).  Protein Structure Determination from Pseudocontact Shifts Using ROSETTA. Journal of molecular biology. Abstract  Download: schmitz12A.pdf (1.03 MB)
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)
Baker, D., Silen J. L., & Agard D. A. (1992).  Protease pro region required for folding is a potent inhibitor of the mature enzyme. Proteins. 12(4), 339-44. Abstract
Das, R., & Baker D. (2009).  Prospects for de novo phasing with de novo protein models. Acta crystallographica. 65(Pt 2), 169-75. Abstract  Download: das09B.pdf (713.43 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)
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)
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)
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)
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)
Baker, D., Bystroff C., Fletterick R. J., & Agard D. A. (1993).  PRISM: topologically constrained phased refinement for macromolecular crystallography. Acta crystallographica. Section D. 49(Pt 5), 429-39. Abstract  Download: baker93A.pdf (3.87 MB)
Bystroff, C., Baker D., Fletterick R. J., & Agard D. A. (1993).  PRISM: application to the solution of two protein structures. Acta crystallographica. Section D. 49(Pt 5), 440-8. Abstract  Download: bystroff93A.pdf (1.05 MB)
Koga, N., Tatsumi-Koga R., Liu G., Xiao R., Acton T. B., Montelione G. T., et al. (2012).  Principles for designing ideal protein structures.. Nature. 491(7423), 222-7. Abstract  Download: nature11600.pdf (2.17 MB)
André, I., Bradley P., Wang C., & Baker D. (2007).  Prediction of the structure of symmetrical protein assemblies. Proceedings of the National Academy of Sciences of the United States of America. 104(45), 17656-61. Abstract  Download: André07A.pdf (1.15 MB)
Wang, C., Vernon R., Lange O., Tyka M., & Baker D. (2010).  Prediction of structures of zinc-binding proteins through explicit modeling of metal coordination geometry. Protein science. 19(3), 494-506. Abstract  Download: wang10A.pdf (571.91 KB)
Wollacott, A. M., Zanghellini A., Murphy P., & Baker D. (2007).  Prediction of structures of multidomain proteins from structures of the individual domains. Protein science. 16(2), 165-75. Abstract  Download: wollacott07A.pdf (1.04 MB)
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)
Barth, P., Wallner B., & Baker D. (2009).  Prediction of membrane protein structures with complex topologies using limited constraints. Proceedings of the National Academy of Sciences of the United States of America. 106(5), 1409-14. Abstract  Download: barth09A.pdf (596.08 KB)
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)
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)
Yi, Q., Bystroff C., Rajagopal P., Klevit R. E., & Baker D. (1998).  Prediction and structural characterization of an independently folding substructure in the src SH3 domain. Journal of molecular biology. 283(1), 293-300. Abstract  Download: yi98A.pdf (785.68 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)
Cooper, S., Khatib F., Treuille A., Barbero J., Lee J., Beenen M., et al. (2010).  Predicting protein structures with a multiplayer online game. Nature. 466(7307), 756-60. Abstract  Download: cooper10A.pdf (1.33 MB)
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)
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)
Terwilliger, T. C., DiMaio F., Read R. J., Baker D., Bunkóczi G., Adams P. D., et al. (2012).  phenix.mr_rosetta: molecular replacement and model rebuilding with Phenix and Rosetta.. Journal of structural and functional genomics. 13(2), 81-90. Abstract
Gu, H., Yi Q., Bray S. T., Riddle D. S., Shiau A. K., & Baker D. (1995).  A phage display system for studying the sequence determinants of protein folding. Protein science. 4(6), 1108-17. Abstract  Download: gu95A.pdf (4.61 MB)