Publications

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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)
Yarov-Yarovoy, V., Baker D., & Catterall W. A. (2006).  Voltage sensor conformations in the open and closed states in ROSETTA structural models of K(+) channels. Proceedings of the National Academy of Sciences of the United States of America. 103(19), 7292-7. Abstract  Download: yarov-yarovoy06A.pdf (3.13 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)
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Wijma, H. J., Floor R. J., Jekel P. A., Baker D., Marrink S. J., & Janssen D. B. (2014).  Computationally designed libraries for rapid enzyme stabilization.. Protein engineering, design & selection : PEDS. 27(2), 49-58. Abstract  Download: Wijma_PEDS_2014.pdf (953.89 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)
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)
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)
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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Tsemekhman, K., Goldschmidt L., Eisenberg D., & Baker D. (2007).  Cooperative hydrogen bonding in amyloid formation. Protein science. 16(4), 761-4. Abstract  Download: tsemekhman07A.pdf (260.96 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)
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)
Thompson, J. M., Sgourakis N. G., Liu G., Rossi P., Tang Y., Mills J. L., et al. (2012).  Accurate protein structure modeling using sparse NMR data and homologous structure information.. Proceedings of the National Academy of Sciences of the United States of America. 109(25), 9875-80. Abstract
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)
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)
Tang, Y., Schneider W. M., Shen Y., Raman S., Inouye M., Baker D., et al. (2010).  Fully automated high-quality NMR structure determination of small (2)H-enriched proteins. Journal of structural and functional genomics. 11(4), 223-32. Abstract  Download: tang10A.pdf (451.53 KB)
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Strauch, E. - M., Fleishman S. J., & Baker D. (2013).  Computational design of a pH-sensitive IgG binding protein. Proceedings of the National Academy of Sciences of the United States of America. Abstract  Download: Strauch-1313605111_PNAS_13W.pdf (1.32 MB)
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)
Song, Y., DiMaio F., Yu-Ruei Wang R., Kim D., Miles C., Brunette T., et al. (2013).  High-resolution comparative modeling with RosettaCM.. Structure (London, England : 1993). 21(10), 1735-42. Abstract
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)
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)
Shen, Y., Lange O., Delaglio F., Rossi P., Aramini J. M., Liu G., et al. (2008).  Consistent blind protein structure generation from NMR chemical shift data. Proceedings of the National Academy of Sciences of the United States of America. 105(12), 4685-90. Abstract  Download: shen08A.pdf (1.01 MB)
Shen, Y., Vernon R., Baker D., & Bax A. (2009).  De novo protein structure generation from incomplete chemical shift assignments. Journal of biomolecular NMR. 43(2), 63-78. Abstract  Download: shen09A.pdf (2.53 MB)
Schonbrun, J., Wedemeyer W. J., & Baker D. (2002).  Protein structure prediction in 2002.. Current opinion in structural biology. 12(3), 348-54. Abstract
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)