Validation of an All-Atom Protein Force Field: From Dipeptides to Larger Peptides

Journal of Physical Chemistry B

Volumn 107, Issue 46, 2003, Pages 12555-12557

  Gnanakaran, S ^a   Garcia, Angel E ^a  

^a LOS ALAMOS NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; COMPUTER SIMULATION; CONFORMATIONS; NUCLEATION; PERTURBATION TECHNIQUES; PROBABILITY; SOLUTIONS; THERMODYNAMICS;

CONFORMATIONAL DISTRIBUTION;

PROTEINS;

EID: 0344962370     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp0359079     Document Type: Article

References (21)

1. Woutersen, S.; Hamm, P. J. Phys. Chem. B 2000, 104, 11316-11320.
2. Woutersen, S.; Mu, Y.; Stock, G.; Hamm, P. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 11254-11258.
3. Schweitzer-Stenner, R.; Eker, F.; Huang, Q.; Griebenow, K. J. Am. Chem. Soc. 2001, 123, 9628-9633.
4. Spek, E.; Olson, C.; Shi, Z.; Kallenbach, N. J. Am. Chem. Soc. 1999, 121, 1, 5571-5572.
5. Shi, Z.; Olson, C.; Rose, G.; Baldwin, R.; Kallenbach, N. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 9190-9195.
6. Woutersen, S.; Pfister, R.; Hamm, P.; Mu, Y.; Kosov, D.; Stock, G. J. Chem. Phys. 2002, 117, 6833-6840.
7. Eker, F.; Cao, X.; Nafie, L.; Schweitzer-Stenner, R. J. Am. Chem. Soc. 2002, 124, 14330-14341.
8. MacKerell, A.; Bashford, D.; Bellott, M.; Dunbrack, R.; Evanseck, J.; Field, M.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; JosephMcCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D.; Prodhom, B.; Reiher, W.; Roux, B.; Schlenkrich, M.; Smith, J.; Stote, R.; Straub, J.; Watanabe, M.; WiorkiewiczKuczera, J.; Yin, D.; Karplus, M. J. Phys. Chem. B 1998, 102, 3586-3616.
9. 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, 5179-5197.
10. Kollman, P. A.; Dixon, R. W.; Cornell, W. D.; Fox, T.; Chipot, C.; Pohorille, A. In Computer simulations of biological systems; Gunsteren, W. v., Ed.; ESCOM: Dordrecht, Netherlands, 1997.
11. Mu, Y.; Kosov, D. S.; Stock, G. J. Phys. Chem. B 2003, 707, 5064-5073.
12. Hu, H.; Elstner, M.; Hermans, J. Proteins 2003, 50, 451-463.
13. Smith, P. J. Chem. Phys. 1999, 111, 5568-5579.
14. Garcia, A.; Sanbonmatsu, K. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 2782-2787.
15. Gnanakaran, S.; Garcia, A. E. Biophys. J. 2003, 84, 1548-1562.
16. Jorgensen, W.; Maxwell, D.; TiradoRives, J. J. Am. Chem. Soc. 1996, 118, 11225-11236.
17. Schuler, L.; Daura. X.; Van Gunsteren, W. J. Comput. Chem. 2001, 22, 1205-1218.
18. Van Gunsteren, W. F.; Billeter, S. R.; Eising, A. A.; Hunenberger, P. H. ; Kruger, P.; Mark, A. E.; Scott, W. R. P.; Tironi, I. G. Biomolecular Simulation: The GROMOS96 Manual and User Guide: Vdf Hochschulverlag AG an der ETH Zurich: Zurich, 1996.
19. Garcia, A. E. Polymer, in press.
20. Gnanakaran, S.; Hochstrasser, R. J. Am. Chem. Soc. 2001, 123, 12886-12898.
21. Poon, C.; Samulski, E.; Weise, C.; Weisshaar, J. J. Am. Chem. Soc. 2000, 122, 5642-5643.