Computational prediction of native protein ligand-binding and enzyme active site sequences

Proceedings of the National Academy of Sciences of the United States of America

Volumn 102, Issue 29, 2005, Pages 10153-10158

  Chakrabarti, Raj ^a,b   Klibanov, Alexander M ^b   Friesner, Richard A ^a  

^a Columbia University ^*  (United States)

^b MASSACHUSETTS INSTITUTE OF TECHNOLOGY   (United States)

Author keywords

Computational protein design; Enzyme design; Protein evolution

Indexed keywords

AMINO ACID; BETA GALACTOSIDASE; BINDING PROTEIN; BIOTIN; ENZYME; LIGAND; M PROTEIN; PEPTIDASE; STREPTAVIDIN; SYNTHETASE;

ACCURACY; ALGORITHM; AMINO ACID SEQUENCE; ARTICLE; BINDING AFFINITY; BINDING SITE; COMPLEX FORMATION; CRYSTALLOGRAPHY; ENZYME ACTIVE SITE; HYDROGEN BOND; LIGAND BINDING; MODEL; MONTE CARLO METHOD; PREDICTION; PRIORITY JOURNAL; PROTEIN STABILITY;

ALGORITHMS; AMINO ACID SEQUENCE; BINDING SITES; BIOPHYSICS; BIOTIN; COMPUTATIONAL BIOLOGY; GLUCOSE; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN CONFORMATION; PROTEINS; STREPTAVIDIN;

EID: 22544451519     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0504023102     Document Type: Article

References (22)

1. Raha, K., Wollacott, A. M., Italia, M. J. & Desjarlais, J. R. (2000) Protein Sci. 9, 1106-1119.
2. Koehl, P. & Levitt, M. (2002) Proc. Natl. Acad. Sci. USA 99, 1280-1285.
3. Kuhlman, B. & Baker, D. (2000) Proc. Natl. Acad. Sci. USA 97, 10383-10388.
4. Jaramillo, A., Wernisch, L., Hery, S. & Wodak, S. J. (2002) Proc. Natl. Acad. Sci. USA 99, 13554-13559.
5. Voigt, C. A., Gordon, D. B. & Mayo, S. L. (2000) J. Mol. Biol. 299, 789-803.
6. Kaminski, G. A., Friesner, R. A., Tirado-Rives, J. & Jorgensen, W. J. (1998) J. Phys. Chem. B 105, 6474-6487.
7. Ghosh, A., Rapp, C. S. & Friesner, R. A. (1998) J. Phys. Chem. B 102, 10983-10990.
8. Gallicchio, E., Zhang, L. Y. & Levy, R. M. (2002) J. Comput. Chem. 5, 517-529.
9. Jacobson, M. F., Kaminski, G. A., Rapp, C. S. & Friesner, R. A. (2002) J. Phys. Chem. B 106, 11673-11680.
10. Xiang, Z. & Honig, B. (2001) J. Mol. Biol. 311, 421-430.
11. Jacobson, M. P., Pincus, D. L., Rapp, C. S., Day, T. J., Honig, B., Shaw, D. E. & Friesner, R. A. (2004) Proteins 55, 351-367.
12. Friesner, R. A., Banks, J. L., Murphy, R. B., Halgren, T. A., Klicic, J. J., Mainz, D. T., Repasky, M. P., Knoll, E. H., Shelley, M., Perry, J. K., et al. (2004) J. Med. Chem. 47, 1739-1749.
13. Weber, P. C., Ohlendorf, D. H., Wendoloski, J. J. & Salemme, F. R. (1989) Science 243, 85-88.
14. Vyas, N. K., Vyas, M. N. & Quiocho, F. A. (1988) Science 242, 1290-1295.
15. Rojas, A. L., Nagem, R. A. P., Neustroev, K. N., Arand, M., Adamska, M., Eneyskaya, E. V., Kulminskaya, A. A., Garratt, R. C., Golubev, A. M. & Polikarpov, I. (2004) J. Mol. Biol. 343, 1281-1292.
16. McDonough, M. A., Anderson, J. W., Silvaggi, N. R., Pratt, R. F., Knox, J. R. & Kelly, J. A. (2002) J. Mol. Biol. 322, 111-122.
17. Hardy, L. W. & Nalivaika, E. (1992) Proc. Natl. Acad. Sci. USA 89, 9725-9729.
18. Gordon, D. B., Marshall, S. A. & Mayo, S. L. (1999) Curr. Opin. Struct. Biol. 9, 509-513.
19. Mooers, B. H. M., Datta, D., Baase, W. A., Zollars, E. S., Mayo, S. L. & Matthews, B. W. (2003) J. Mol. Biol. 332, 741-756.
20. Desjarlais, J. R. & Clarke, N. D. (1998) Curr. Opin. Struct. Biol. 8, 471-476.
21. Desmet, J., De Maeyer, M., Hazes, B. & Lasters, I. (1992) Nature 356, 539-542.
22. Looger, L. L., Dwyer, M. A. Smith, J. I. & Hellinga, H. W. (2003) Nature 423, 185-189.