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Дата изменения: Mon Dec 10 13:50:38 2012
Дата индексирования: Sun Feb 3 03:40:24 2013
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Rosetta

2012

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Rosetta Rohl, C. A., Strauss, C. E., Misura, K. M., and Baker, D. (2004) Protein structure prediction using Rosetta. Methods Enzymol. 383, 6693. 1 J. J. Gray, S. Moughon, C. Wang, O. Schueler-Furman, B. Kuhlman, C. A. Rohl, and D. Baker, J. Mol. Biol. 331, 281 (2003). 2 C. A. Rohl, C. E. M. Strauss, D. Chivian, and D. Baker, Proteins Struct. Funct. Genet. In press (2004). 3 J. R. Gunn, J. Chem. Phys. 106, 4270 (1997). 13 R. Engh and R. Huber, Acta Crystallogr. A 47, 392 (1991). 4 R. L. Dunbrack and F. E. Cohen, Protein Sci. 6, 1661 (1997). 5 K. T. Simons, C. Kooperberg, E. Huang, and D. Baker, J. Mol. Biol. 268, 209 (1997). 6 K. T. Simons, I. Ruczinski, C. Kooperberg, B. Fox, C. Bystroff, and D. Baker, Proteins Struct. Funct. Genet. 35, 82 (1999). 7 T. Lazaridis and M. Karplus, Proteins Struct. Funct. Genet. 35, 133 (1999). 8 Z. Li and H. A. Scheraga, Proc. Natl. Acad. Sci. USA 84, 6611 (1987). 9. Qian, B., Raman, S., Das, R., Bradley, P., McCoy, A. J., Read, R. J., and Baker, D. (2007) High-resolution structure prediction and the crystallographic phase problem. Nature 450, 259264. 10. Gray, J. J., Moughon, S., Wang, C., Schueler-Furman, O., Kuhlman, B., Rohl, C. A., and Baker, D. (2003) Protein-protein docking with simultaneous optimization of rigid-body displacement and sidechainconformations. J. Mol. Biol. 331, 281299. 11. Roche, O., Kiyama, R., and Brooks, C. L., III (2001) Ligand-protein database: Linking protein-ligand complex structures to binding data. J. Med. Chem. 44, 35923598. 12. Burguete, A. S., Fenn, T. D., Brunger, A. T., and Pfeffer, S. R. (2008) Rab and Arl GTPase family members cooperate in the localization of the golgin GCC185. Cell 132, 286298. 13. Kuhlman, B., Dantas, G., Ireton, G. C., Varani, G., Stoddard, B. L., and Baker, D. (2003) Design of a novel globular protein fold with atomic-level accuracy. Science 302, 13641368. 14. Dantas, G., Corrent, C., Reichow, S. L., Havranek, J. J., Eletr, Z. M., Isern, N. G., Kuhlman, B., Varani, G., Merritt, E. A., and Baker, D. (2007) High-resolution structural and thermodynamic analysis of extreme stabilization of human procarboxypeptidase by computational protein design. J. Mol. Biol. 366, 12091221. 15. Chevalier, B. S., Kortemme, T., Chadsey, M. S., Baker, D., Monnat, R. J., and Stoddard, B. L. (2002) Design, activity, and structure of a highly specific artificial endonuclease. Mol. Cell 10, 895905. 16. Joachimiak, L. A., Kortemme, T., Stoddard, B. L., and Baker, D. (2006) Computational design of a new hydrogen bond network and at least a 300-fold specificity switch at a protein-protein interface. J. Mol. Biol. 361, 195208. 17. Jiang, L., Althoff, E. A., Clemente, F. R., Doyle, L., Rothlisberger, D., Zanghellini, A., Gallaher, J. L., Betker, J. L., Tanaka, F., Barbas, C. F., Hilvert, D., Houk,K.N., Stoddard, B. L., and Baker, D. (2008) De novo computational design of retro-aldol enzymes. Science 319, 13871391. 18. Sircar, A., and Gray, J. J. (2010) SnugDock: Paratope structural optimization during antibody-antigen docking compensates for errors in antibody homology models. PLoS Comput. Biol. 6, e1000644.