Dramatic performance enhancements for the FASTER optimization algorithm

Journal of Computational Chemistry

Volumn 27, Issue 10, 2006, Pages 1071-1075

  Allen, Benjamin D ^a   Mayo, Stephen L ^b  

^a California Institute of Technology   (United States)

^b HOWARD HUGHES MEDICAL INSTITUTE   (United States)

Author keywords

Combinatorial optimization; FASTER; Monte Carlo; Protein design; Side chain placement

Indexed keywords

COMBINATORIAL OPTIMIZATION; FASTER; MONTE CARLO; PROTEIN DESIGN; SIDE-CHAIN PLACEMENT;

ALGORITHMS; COMPUTATION THEORY; MONTE CARLO METHODS; OPTIMIZATION; PERTURBATION TECHNIQUES; PROTEINS;

COMBINATORIAL MATHEMATICS;

PROTEIN;

ALGORITHM; ARTICLE; BIOLOGY; CHEMISTRY; COMPUTER PROGRAM; COMPUTER SIMULATION; MONTE CARLO METHOD; PROTEIN CONFORMATION;

ALGORITHMS; COMPUTATIONAL BIOLOGY; COMPUTER SIMULATION; MONTE CARLO METHOD; PROTEIN CONFORMATION; PROTEINS; SOFTWARE;

EID: 33745614865     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.20420     Document Type: Article

References (23)

1. Voigt, C. A.: Gordon, D. B.; Mayo, S. L. J Mol Biol 2000, 299, 789.
2. Metropolis, N.; Rosenbluth, A. W.; Rosenbluth, M. N.; Teller, A. H.; Teller, E. J Chem Phys 1953, 21, 1087.
3. Kirkpatrick, S.; Gelatt, C. D.; Vecchi, M. P. Science 1983, 220, 671.
4. Kuhlman, B.; Dantas, G.; Ireton, G. C.; Varani, G.; Stoddard, B. L.; Baker, D. Science 2003, 302, 1364.
5. Desmet, J.; De Maeyer, M.; Hazes, B.; Lasters, I. Nature 1992, 356, 539.
6. Gordon, D. B.; Hom, G. K.; Mayo, S. L.; Pierce, N. A. J Comp Chem 2002, 232.
7. Koehl, P.; Delarue, M. J Mol Biol 1994, 239, 249.
8. Jones, David T. Protein Sci 1994, 3, 567.
9. Desjarlais, J. R.; Handel, T. M. Protein Sci 1995, 4, 2006.
10. Desmet, J.; Spriet, J.; Lasters, I. Proteins 2002, 48, 31.
11. Elrod-Erickson, M.; Rould, M. A.; Nekludova, L.; Pabo, C. O. Structure 1996, 4, 1171.
12. Ranganathan, R.; Lu, K. P.; Hunter, T.; Noel, J. P. Cell 1997, 89, 875.
13. Gallagher, T.; Alexander, P.; Bryan, P.; Gilliland, G. L. Biochemistry 1994, 33, 4721.
14. Mueller, U.; Perl, D.; Schmid, F. X.; Heinemann, U. J Mol Biol 2000, 297, 975.
15. Dahiyat, B. I.; Mayo, S. L. Science 1997, 278, 82.
16. Kraemer-Pecore, C. M.; Lecomte, J. T. J.; Desjarlais, J. R. Protein Sci 2003, 12, 2194.
17. Malakauskas, S. M.; Mayo, S. L. Nat Struct Biol 1998, 5, 470.
18. Perl, D.; Schmid, F. X. J Mol Biol 2001, 313, 343.
19. Word, J. M.; Lovell, S. C.; Richardson, J. S.; Richardson, D. C. J Mol Biol 1999, 285, 1735.
20. Dunbrack, R. L., Jr.; Cohen, F. E. Protein Sci 1997, 6, 1661.
21. Gordon, D. B.; Marshall, S. A.; Mayo, S. L. Curr Opin Struct Biol 1999, 9, 509.
22. De Maeyer, M.; Desmet, J.; Lasters, I. Fold Des 1997, 2, 53.
23. Goldstein, R. F. Biophys J 1994, 66, 1335.