Empirical force-field assessment: The interplay between backbone torsions and noncovalent term scaling

Journal of Computational Chemistry

Volumn 26, Issue 7, 2005, Pages 682-690

  Sorin, Eric J ^a   Pande, Vijay S ^a  

^a STANFORD UNIVERSITY   (United States)

Author keywords

AMBER; Distributed computing; protein folding; Fs peptide; Molecular dynamics

Indexed keywords

AMBER; CHEMICAL BONDS; COMPUTER SIMULATION; CONFORMATIONS; DISTRIBUTED COMPUTER SYSTEMS; MOLECULAR DYNAMICS; NITROGEN COMPOUNDS; POLYPEPTIDES; TORSIONAL STRESS;

BIOPHYSICAL THEORIES; FS PEPTIDE; PROTEIN FOLDINGS; QUANTUM COMPUTATION;

THERMODYNAMICS;

PEPTIDE; POLYALANINE; PROTEIN;

ALGORITHM; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; PROTEIN CONFORMATION; THERMODYNAMICS; TORSION;

ALGORITHMS; COMPUTER SIMULATION; MODELS, MOLECULAR; PEPTIDES; PROTEIN CONFORMATION; PROTEINS; THERMODYNAMICS; TORSION;

EID: 85047692291     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/jcc.20208     Document Type: Article

References (37)

1. Rhee, Y. M.; Sorin, E. J.; Jayachandran, G.; Lindahl, E.; Pande, V. S. Proc Natl Acad Sci USA 2004, 101, 6456.
2. Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. J Am Chem Soc 1996, 118, 11225.
3. MacKerell, A. D., Jr.; Bashford, D.; Bellott, M.; Dunbrack, R. L., Jr.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E., III; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiórkiewicz-Kuczera, J.; Yin, D.; Karplus, M. J Phys Chem B 1998, 102, 3586.
4. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Gould, I. R.; Merz, K. M.; Ferguson, D. M.; Spellmeyer, D. C.; Fox, T.; Caldwell, J. W.; Kollman, P. A. J Am Chem Soc 1995, 117, 5179.
5. Kollman, P.; Dixon, R.; Cornell, W.; Fox, T.; Chipot, C.; Pohorille, A. In Computer Simulations of Biomolecular Systems: Theoretical and Experimental Applications; van Gunsteren, W. F.; Wiener, P. K., Eds.; Escom, Dordrecht, 1997, p. 83.
6. Wang, J.; Cieplak, P.; Kollman, P. A. J Comp Chem 2000, 21, 1049.
7. Garcia, A. E.; Sanbonmatsu, K. Y. Proc Natl Acad Sci USA 2001, 99, 2782.
8. Duan, Y.; Wu, C.; Chowdhury, S.; Lee, M. C.; Xiong, G.; Zhang, W.; Yang, R.; Cieplak, P.; Luo, R.; Lee, T.; Caldwell, J.; Wang, J.; Kollman, P. J Comp Chem 2003, 24, 1999.
9. Duan, Y.; Kollman, P. A. Science 1998, 282, 740.
10. Mayor, U.; Guydosh, N. R.; Johnson, C. M.; Grossmann, J. G.; Sato, S.; Jas, G. S.; Freund, S. M. V.; Alonsok, D. O. V.; Daggett, V.; Fersht, A. R. Nature 2003, 421, 863.
11. Zhou, R.; Huang, X.; Margulis, C. J.; Berne, B. J. Science 2004, 305, 1605.
12. Sorin, E. J.; Pande, V. S. Biophys J 2004, 88, in press.
13. Lindahl, E.; Hess, B.; van der Spoel, D. J Mol Mod 2001, 7, 306.
14. Zagrovic, B.; Sorin, E. J.; Pande, V. J Mol Biol 2001, 313, 151.
15. Nymeyer, H.; Garcia, A. E. Proc Natl Acad Sci USA 2003, 100, 13934.
16. Garcia, A. E. Polymer 2004, 45, 669.
17. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J Chem Phys 1983, 79, 926.
18. Berendsen, H.; Postma, J.; Vangunsteren, W.; Dinola, A.; Haak, J. J Chem Phys 1984, 81, 3684.
19. Thompson, P. A.; Eaton, W. A.; Hofrichter, J. Biochemistry 1997, 36, 9200.
20. Ianoul, A.; Mikhonin, A.; Lednev, I. K.; Asher, S. A. J Phys Chem A 2002, 106, 3621.
21. Hess, B.; Bekker, H.; Berendsen, H. J. C.; Fraaije, J. G. E. M. J Comp Chem 1997, 18, 1463.
22. Qian, H.; Schellman, J. A. J Phys Chem 1992, 96, 3987.
23. Williams, S.; Causgrove, T. P.; Gilmanshin, R.; Fang, K. S.; Callender, R. H.; Woodruff, W. H.; Dyer, R. B. Biochemistry 1996, 35, 691.
24. Brooks, C. L. J Phys Chem 1996, 100, 2546.
25. Kabsch, W.; Sander, C. Biopolymers 1983, 22, 2577.
26. Zagrovic, B.; Jayachandran, G.; Millett, I. S.; Doniach, S.; Pande, V. S. 2004, in preparation.
27. Millhauser, G. L.; Stenland, C. J.; Hanson, P.; Bolin, K. A.; van de Yen, F. J. M. J Mol Biol 1997, 267, 963.
28. Armen, R.; Alonso, D. O. V.; Daggett, V. Protein Sci 2003, 12, 1145.
29. Drozdov, A. N.; Grossfield, A.; Pappu, R. V. J Am Chem Soc 2003, 126, 2574.
30. Kentsis, A.; Mezei, M.; Gindin, T.; Osman, R. Proteins 2004, 55, 493.
31. Mezei, M.; Fleming, P. J.; Srinivasan, R.; Rose, G. D. Proteins 2004, 55, 502.
32. Shi, Z.; Olson, C. A.; Rose, G. D.; Baldwin, R. L.; Kallenbach, N. R. Proc Natl Acad Sci USA 2002, 99, 9190.
33. Weise, C. F.; Weisshaar, J. C. J Phys Chem B 2003, 107, 3265.
34. Ohkubo, Y. Z.; Brooks, C. L. Proc Natl Acad Sci USA 2003, 100, 13916.
35. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J Comp Chem 1983, 4, 187.
36. Zagrovic, B.; Sorin, E. J.; Millett, I. S.; van Gunsteren, W. F.; Doniach, S.; Pande, V. S., Proc Natl Acad Sci USA 2005, to be published.
37. Zaman, M. H.; Shen, M.-Y.; Berry, R. S.; Freed, K. F.; Sosnick, T. R. J Mol Biol 2003, 331, 693.