Publications

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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)
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)
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)
Baker, D., & Sali A. (2001).  Protein structure prediction and structural genomics.. Science (New York, N.Y.). 294(5540), 93-6. Abstract
Schonbrun, J., Wedemeyer W. J., & Baker D. (2002).  Protein structure prediction in 2002.. Current opinion in structural biology. 12(3), 348-54. Abstract
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)
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)
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)
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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)
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)
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)
Han, K. F., & Baker D. (1995).  Recurring local sequence motifs in proteins. Journal of molecular biology. 251(1), 176-87. Abstract  Download: han95A.pdf (297.22 KB)
Thyme, S., & Baker D. (2014).  Redesigning the Specificity of Protein-DNA Interactions with Rosetta.. Methods in molecular biology (Clifton, N.J.). 1123, 265-82. Abstract  Download: Thyme_2014.pdf (413.9 KB)
Althoff, E. A., Wang L., Jiang L., Giger L., Lassila J. K., Wang Z., et al. (2012).  Robust design and optimization of retroaldol enzymes.. Protein science : a publication of the Protein Society. 21(5), 717-26. Abstract
Wang, C., Schueler-Furman O., Andre I., London N., Fleishman S. J., Bradley P., et al. (2007).  RosettaDock in CAPRI rounds 6-12. Proteins. 69(4), 758-63. Abstract  Download: wang07B.pdf (214.39 KB)
Davis, I. W., & Baker D. (2009).  RosettaLigand docking with full ligand and receptor flexibility. Journal of molecular biology. 385(2), 381-92. Abstract  Download: davis09B.pdf (1.36 MB)
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Kim, D. E., Blum B., Bradley P., & Baker D. (2009).  Sampling bottlenecks in de novo protein structure prediction. Journal of molecular biology. 393(1), 249-60. Abstract  Download: kim09A.pdf (1.12 MB)
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)
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)
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)
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)
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)
Das, R., André I., Shen Y., Wu Y., Lemak A., Bansal S., et al. (2009).  Simultaneous prediction of protein folding and docking at high resolution. Proceedings of the National Academy of Sciences of the United States of America. 106(45), 18978-83. Abstract  Download: das09A.pdf (1.57 MB)
Yarov-Yarovoy, V., DeCaen P. G., Westenbroek R. E., Pan C. - Y., Scheuer T., Baker D., et al. (2012).  Structural basis for gating charge movement in the voltage sensor of a sodium channel. Proceedings of the National Academy of Sciences of the United States of America. 109(2), E93-102. Abstract  Download: yarov-yarovoy12A.pdf (2.46 MB)
Chen, D. - H., Baker M. L., Hryc C. F., DiMaio F., Jakana J., Wu W., et al. (2011).  Structural basis for scaffolding-mediated assembly and maturation of a dsDNA virus. Proceedings of the National Academy of Sciences of the United States of America. 108(4), 1355-60. Abstract  Download: chen11A.pdf (2.71 MB)
Das, R., Kudaravalli M., Jonikas M., Laederach A., Fong R., Schwans J. P., et al. (2008).  Structural inference of native and partially folded RNA by high-throughput contact mapping. Proceedings of the National Academy of Sciences of the United States of America. 105(11), 4144-9. Abstract  Download: das08A.pdf (806.02 KB)