Publications

Found 387 results

2009
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)
Murphy, P. M., Bolduc J. M., Gallaher J. L., Stoddard B. L., & Baker D. (2009).  Alteration of enzyme specificity by computational loop remodeling and design. Proceedings of the National Academy of Sciences of the United States of America. 106(23), 9215-20. Abstract  Download: murphy09A.pdf (954.03 KB)
Havranek, J. J., & Baker D. (2009).  Motif-directed flexible backbone design of functional interactions. Protein science. 18(6), 1293-305. Abstract  Download: havranek09A.pdf (753.33 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)
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)
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)
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)
Kidd, B. A., Baker D., & Thomas W. E. (2009).  Computation of conformational coupling in allosteric proteins. PLoS computational biology. 5(8), e1000484. Abstract  Download: kidd09A.pdf (484.92 KB)
2008
André, I., Strauss C. E. M., Kaplan D. B., Bradley P., & Baker D. (2008).  Emergence of symmetry in homooligomeric biological assemblies. Proceedings of the National Academy of Sciences of the United States of America. 105(42), 16148-52. Abstract  Download: andré08A.pdf (588.8 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)
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)
McBeth, C., Seamons A., Pizarro J. C., Fleishman S. J., Baker D., Kortemme T., et al. (2008).  A new twist in TCR diversity revealed by a forbidden alphabeta TCR. Journal of molecular biology. 375(5), 1306-19. Abstract  Download: mcbeth08A.pdf (5.02 MB)
Das, R., & Baker D. (2008).  Macromolecular modeling with rosetta. Annual review of biochemistry. 77, 363-82. Abstract  Download: das08A.pdf (1.13 MB)
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)
2007
Das, R., & Baker D. (2007).  Automated de novo prediction of native-like RNA tertiary structures. Proceedings of the National Academy of Sciences of the United States of America. 104(37), 14664-9. Abstract  Download: das07A.pdf (1.29 MB)
Barth, P., Schonbrun J., & Baker D. (2007).  Toward high-resolution prediction and design of transmembrane helical protein structures. Proceedings of the National Academy of Sciences of the United States of America. 104(40), 15682-7. Abstract  Download: barth07A.pdf (728.74 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)
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)
Li, J., Shinjo M., Matsumura Y., Morita M., Baker D., Ikeguchi M., et al. (2007).  An alpha-helical burst in the src SH3 folding pathway. Biochemistry. 46(17), 5072-82. Abstract  Download: li07A.pdf (493.42 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)
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)
2006
Goobes, G., Goobes R., Schueler-Furman O., Baker D., Stayton P. S., & Drobny G. P. (2006).  Folding of the C-terminal bacterial binding domain in statherin upon adsorption onto hydroxyapatite crystals. Proceedings of the National Academy of Sciences of the United States of America. 103(44), 16083-8. Abstract  Download: goobes06A.pdf (725.15 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)
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)
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)
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)
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)
Arakaki, T., Le Trong I., Phizicky E., Quartley E., Detitta G., Luft J., et al. (2006).  Structure of Lmaj006129AAA, a hypothetical protein from Leishmania major. Acta crystallographica. Section F, Structural biology and crystallization communications. 62(Pt 3), 175-9. Abstract  Download: structureoflmaj006129aaa_Baker2006.pdf (639.08 KB)
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)
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)
2005
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)
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)