Publications

Sort by: [ Author  (Asc)] Title Type Year
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 
R
S
S, R., B Q., D B., & RC W. (2008).  Advances in Rosetta Protein Structure Prediction on Massively Parallel Systems. Journal of Research and Development . 52(1-2):7-17, Abstract  Download: raman08A.pdf (446.3 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)
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)
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)
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)
Schonbrun, J., Wedemeyer W. J., & Baker D. (2002).  Protein structure prediction in 2002.. Current opinion in structural biology. 12(3), 348-54. Abstract
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)
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)
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)
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
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)
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)
T
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)
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)
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)
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
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)
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)
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)
U
V
W
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)
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)
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)