Preprocessing of rotamers for protein design calculations

Journal of Computational Chemistry

Volumn 25, Issue 14, 2004, Pages 1797-1800

  Shah, Premal S ^a   Hom, Geoffrey K ^a   Mayo, Stephen L ^b  

^a CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

^b HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

Dead end elimination; Protein design; Side chain placement

Indexed keywords

DEAD END ELIMINATION; PROTEIN DESIGN; SIDE CHAIN PLACEMENTS;

ALGORITHMS; COMPUTATIONAL METHODS; MATHEMATICAL MODELS; MONTE CARLO METHODS; THEOREM PROVING;

PROTEINS;

PROTEIN;

ALGORITHM; ARTICLE; CHEMISTRY; PROTEIN CONFORMATION;

ALGORITHMS; PROTEIN CONFORMATION; PROTEINS;

EID: 5444230250     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/jcc.20097     Document Type: Article

References (30)

1. Janin, J.; Wodak, S. J Mol Biol 1978, 125, 357.
2. Ponder, J. W.; Richards, F. M. J Mol Biol 1987, 193, 775.
3. Dunbrack, R. L., Jr.; Karplus, M. J Mol Biol 1993, 230, 543-574.
4. Desmet, J.; De Maeyer, M.; Hazes, B.; Lasters, I. Nature 1992, 356, 539.
5. Dahiyat, B. I.; Mayo, S. L. Protein Sci 1996, 5, 895.
6. Dahiyat, B. I.; Mayo, S. L. Proc Natl Acad Sci USA 1997, 94, 10172.
7. Dahiyat, B. I.; Mayo, S. L. Science 1997, 278, 82.
8. Malakauskas, S. M.; Mayo, S. L. Nat Struct Biol 1998, 5, 470.
9. Bolon, D. N.; Mayo, S. L. Proc Natl Acad Sci USA 2001, 98, 14274.
10. Marshall, S. A.; Mayo, S. L. J Mol Biol 2001, 305, 619.
11. Looger, L. L.; Dwyer, M. A.; Smith, J. J.; Hellinga, H. W. Nature 2003, 423, 185.
12. Gordon, D. B.; Mayo, S. L. J Comput Chem 1998, 19, 1505.
13. Pierce, N. A.; Spriet, J. A.; Mayo, S. L. J Comput Chem 2000, 21, 999.
14. Looger, L. L.; Hellinga, H. W. J Mol Biol 2001, 307, 429.
15. Gordon, D. B.; Horn, G. K.; Mayo, S. L.; Pierce, N. A. J Comput Chem 2003, 24, 232.
16. Metropolis, N.; Rosenbluth, A. W.; Rosenbluth, M. N.; Teller, A. H.; Teller, E. J Chem Phys 1953, 21, 1087.
17. Kirkpatrick, S.; Gelatt, C. D.; Vecchi, M. P. Science 1983, 220, 671.
18. Holland, J. H. Adaptation in Natural and Artificial Systems; The MIT Press: Cambridge, MA, 1992.
19. Desjarlais, J. R.; Handel, T. M. Protein Sci 1995, 4, 2006.
20. Koehl, P.; Delarue, M. J Mol Biol 1994, 239, 249.
21. Koehl, P.; Delarue, M. Curr Opin Struct Biol 1996, 6, 222.
22. Gordon, D. B.; Mayo, S. L. Struct Fold Des 1999, 7, 1089.
23. De Maeyer, M.; Desmet, J.; Lasters, I. Fold Des 1997, 2, 53.
24. Voigt, C. A.; Gordon, D. B.; Mayo, S. L. J Mol Biol 2000, 299, 789.
25. Gallagher, T.; Alexander, P.; Bryan, P.; Gilliland, G. L. Biochemistry 1994, 33, 4721.
26. Clarke, N. D.; Kissinger, C. R.; Desjarlais, J.; Gilliland, G. L.; Pabo, C. O. Protein Sci 1994, 3, 1779.
27. Desmet, J.; Spriet, J.; Lasters, I. Proteins 2002, 48, 31.
28. Gordon, D. B.; Marshall, S. A.; Mayo, S. L. Curr Opin Struct Biol 1999, 9, 509.
29. Street, A. G.; Mayo, S. L. Struct Fold Des 1999, 7, R105.
30. Street, A. G.; Mayo, S. L. Fold Des 1998, 3, 253.