Computer simulation of Met-enkephalin using explicit atom and united atom potentials: Similarities, differences, and suggestions for improvement

Journal of Physical Chemistry B

Volumn 107, Issue 7, 2003, Pages 1685-1691

  Zaman, Muhammad H ^a,b   Shen, Min Yi ^a,c   Berry, R Stephen ^a,c   Freed, Karl F ^a,c  

^a UNIVERSITY OF CHICAGO   (United States)

^b UNIVERSITY OF CHICAGO   (United States)

^c UNIVERSITY OF CHICAGO   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ATOMS; COMPUTER SIMULATION; CONFORMATIONS; PROTEINS;

ATOM FORCE FIELDS;

MOLECULAR DYNAMICS;

EID: 0037456294     PISSN: 10895647     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp026994s     Document Type: Article

References (36)

1. Williams, D. E. J. Chem. Phys. 1967, 47, 4680.
2. Ryckaert, J. P.; Bellemans, A. Faraday Discuss. Chem. Soc. 1978, 66, 95.
3. Martin, M. G.; Siepmann, J. I. J. Phys. Chem. B 1998, 102, 2569.
4. Zagrovic, B.; Sorin, E. J.; Pande, V. S. J. Mol. Biol. 2001, 313, 151.
5. Shirts, M. R.; Pande, V. S. Phys. Rev. Lett. 2001, 86, 4983.
6. Yoon, D. Y.; Smith, G. D.; Matsuda, T. J. Chem. Phys. 1993, 98, 10037.
7. Smith, G. D.; Yoon, D. Y. J. Chem. Phys. 1994, 100, 649.
8. Martin, M. G.; Siepmann, J. I. J. Phys. Chem. B 1999, 103, 4508.
9. Karayiannis, N. C.; Mavrantzas, V. G.; Theodorou, D. N. Phys. Rev. Lett. 2002, 88, 105503-1.
10. Sides, S. W.; Curro, J.; Grest, G. S.; Stevens, M. J.; Soddenmann, T.; Habenschuss, A.; Londono, J. D. Macromolecules 2002, 35, 6455.
11. Mu, Y.; Stock, G. J. Phys. Chem. B 2002, 106, 5294.
12. Mu, Y.; Kosov, D. S.; Stock, G. J. Phys. Chem. B, submitted for publication, 2002.
13. Bryant Z.; Pande, V. S.; Rokshar, D. S. Biophys. J. 2000, 78, 584.
14. Shen, M. Y.; Freed, K. F. Biophys. J. 2002, 82, 1791.
15. Shen, M. Y.; Freed, K. F. Proteins: Struct., Funct., Genet. 2002, 49, 439.
16. Hughes, J.; Smith, T. W.; Kosterlitz, H. W.; Fothergill, L. A.; Moran, B. A.; Morris, H. R. Nature (London) 1975, 258, 577.
17. Smith, G. D.; Griffin, J. F. Science (Washington, D.C.) 1978, 199, 1214.
18. Roques, B. P.; Garbay-Jaureguiberry, C.; Oberlin, R.; Anteunis, M.; Lala, A. K. Nature (London) 1976, 262, 778.
19. Deber, C. M.; Behnam, B. A. Proc. Natl. Acad. Sci. U.S.A. 1984, 81, 61.
20. Wang, Y.; Kuczera, K. J. Phys. Chem. 1996, 100, 2555.
21. Graham, W. H.; Carter, E. S.; Hicks, R. P. Biopolymers 1992, 32, 1755.
22. Kollman, P.; Dixon, R.; Cornell, W.; Fox, T.; Chipot, C.; Pohorille, A. In Computer Simulations of Biomolecular System 3; van Gunstern, W. F., Wiener, P. K., Wilson, A. J., Eds.; Kluwer Academic: Dordrecht, The Netherlands, 1997; p 83.
23. Weiner, S. J.; Kollman, P. A.; Nguyen, D. T.; Case, D. A. J. Comput. Chem. 1986, 7, 230.
24. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, J.; Karplus, M. J. Comput. Chem. 1983, 4, 187.
25. MacKerrell, A. D.; Bashford, D.; Bellot, M.; Dunbrack, R. L.; Evvanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, K.; Kuczera, F.; Lau, T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E.; Rounx, B.; Schlenkrich, M.; Smith, J. C.; Store, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. J. Phys. Chem. B 1998, 102, 3586.
26. Jorgensen, W. L.; Tirado-Rives, J. J. Am. Chem. Soc. 1988, 110, 1657.
27. Neria, E.; Fischer, S.; Karplus, M. J. J. Chem. Phys. 1996, 105, 1902.
28. Ooi, T.; Oobatake, G.; Nemethy, G.; Scheraga, H. A. Proc. Natl. Acad. Sci. U.S.A. 1987, 84, 3086.
29. Pastor, R. W.; Karplus, M. J. Phys. Chem. 1988, 92, 2636.
30. Allen, M. P.; Tildesley, D. J. Computer Simulation of Liquids; Oxford University Press: Oxford, U.K., 1987.
31. Ponder, J. W.; Rubenstein, S.; Kundrot, C.; Huston, S.; Dudek, M.; Kong, Y.; Hart, R.; Hodson, M.; Pappu, R.; Mooiji, W.; Loeffler, G. TINKER: Software Tools for Molecular Design, version 3.7; Washington University: St. Louis, MO, 1999.
32. Beachy, M. D.; Chasman, D.; Murphy, R. B.; Halgren, T. A.; Friesner, R. A. J. Am. Chem. Soc. 1997, 119, 5908.
33. Zwanzig, R.; Aliwadi, N. K. Phys. Rev. 1969, 182, 280.
34. Pütz, M.; Curro, J. G.; Grest, G. S. J. Chem. Phys. 2001, 114, 2847.
35. Pappu, R. V.; Rose, G. D. Protein Sci. 2002, 11, 2437.
36. Sanbonmatsu, K. Y.; Garcia, A. E. Proteins: Struct., Funct., Genet. 2002, 46, 225.