Probability distributions for complex systems: Adaptive umbrella sampling of the potential energy

Journal of Physical Chemistry B

Volumn 102, Issue 5, 1998, Pages 865-880

  Bartels, Christian ^a   Karplus, Martin ^a,b  

^a UNIVERSITÉ DE STRASBOURG   (France)

^b HARVARD UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACIDS; COMPUTER SIMULATION; CONFORMATIONS; MOLECULAR STRUCTURE;

ADAPTIVE UMBRELLA SAMPLING; THREONINE DIPEPTIDE;

MOLECULAR DYNAMICS;

EID: 0031648813     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp972280j     Document Type: Article

References (51)

1. Brooks, C. L., III; Karplus, M.; Pettitt, B. M. Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics. John Wiley & Sons: New York, 1988.
2. McCammon, J. A.; Harvey, S. Dynamics of Proteins and Nucleic Acids; Cambridge University Press: Cambridge, U.K., 1987.
3. Elber, R. Curr. Opin. Struct. Biol. 1996, 6, 232.
4. Boczko, E. M.; Brooks, C. L., III Science 1995, 269, 393.
5. Boczko, E. M.; Brooks, C. L., III J. Phys. Chem. 1993, 97, 4509.
6. Bartels, C.; Karplus, M. J. Comput. Chem. 1997, 18, 1450.
7. Ferrenberg, A. M. Thesis, Carnegie-MELLON University, Pittsburgh, PA, Order Number 9006207, 1989.
8. Kumar, S.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A.; Rosenberg, J. M. J. Comput. Chem. 1992, 13, 1011.
9. Torrie, G. M.; Valleau, J. P. J. Comput. Phys. 1977, 23, 187.
10. Hooft, R. W. W. J. Chem. Phys. 1992, 97, 6690.
11. Mezei, M. J. Comput. Phys. 1987, 68, 237.
12. Straatsma, T. P.; McCammon, J. A. J. Chem. Phys. 1994, 101, 5032.
13. Tsujishita, H.; Moriguchi, I.; Hirono, S. J. Phys. Chem. 1993, 97, 4416.
14. Liu, Z.; Berne, B. J. J. Chem. Phys. 1993, 99, 6071.
15. Roitberg, A.; Elber, R. J. Chem. Phys. 1991, 95, 9277.
16. Verkhivker, G.; Elber, R.; Nowak, W. J. Chem. Phys. 1992, 97, 7838.
17. Piela, L.; Kostrowicki, J.; Scheraga, H. A. J. Phys. Chem. 1989, 93, 3339.
18. Straub, J. E.; Ma, J.; Amara, P. J. Chem. Phys. 1995, 103, 1574.
19. Lee, J. Phys. Rev. Lett. 1993, 71, 211.
20. Lyubartsev, A. P.; Martsinovski, A. A.; Shevkunov, S. V.; Vorontsov-Velyaminov, P. N. J. Chem. Phys. 1992, 96, 1776.
21. Berg, B. A. Int. J. Mod. Phys. 1992, C3, 1083.
22. Berg, B. A.; Neuhaus, T. Phys. Rev. Lett. 1992, 68, 9.
23. Hansmann, U. H. E.; Okamoto, Y. J. Comput. Chem. 1993, 14, 1333.
24. Hao, M.-H.; Scheraga, H. A. J. Phys. Chem. 1994, 98, 4940.
25. Kidera, A. Proc. Natl. Acad. Sci. U.S.A. 1995, 92, 9886.
26. Hansmann, U. H. E.; Okamoto, Y. Physica A 1994, 212, 415.
27. Bradbury, A. F.; Smyth, D. G.; Snell, C. R. Nature 1976, 260, 165.
28. Camerman, A.; Mastropaolo, D.; Karle, I.; Karle, J.; Camerman, N. Nature 1983, 306, 447.
29. Nakajima, N.; Nakamura, H.; Kidera, A. J. Phys. Chem. 1997, 101, 817.
30. Bartels, C.; Stote, R. H.; Karplus, M. Manuscript in preparation.
31. Kumar, S.; Payne, P. W.; Vásquez, M. J. Comput. Chem. 1996, 17, 1269.
32. Gelman, A.; Carlin, J. B.; Stern, H. S., Rubin, D. B. Bayesian Data Analysis; Chapman & Hall: London, 1995.
33. Krengel, U. Einführung in die Wahrscheinlichkeitstheorie und Statistik. Vieweg: Braunschweig/Wiesbaden, Germany, 1991.
34. Atkins, P. W. Physical Chemistry; Oxford University Press: Oxford, 1987.
35. Huang, K. Statistical Mechanics. John Wiley & Sons: New York, 1987.
36. Karplus, M.; Shakhnovich, E. In Protein Folding: Theoretical Studies of Thermodynamics and Dynamics; Creighton, T. E., Ed.; W. H. Freeman and Company: New York, 1992.
37. Sali, A.; Shakhnovich, E.; Karplus, M. Nature 1994, 369, 248.
38. Valleau, J. P.; Torrie, G. M. In A Guide to Monte Carlo for Statistical Mechanics: 2. Byways; Berne, B. J., Ed.; Plenum Press: New York, 1977.
39. Berg, B. A.; Hansmann, U. H. E.; Okamoto, Y. J. Phys. Chem. 1995, 99, 2236.
40. Hansmann, U. H. E.; Okamoto, Y.; Eisenmenger, F. Chem. Phys. Lett. 1996, 259, 321.
41. Hoover, W. G. Phys. Rev. A 1985, 31, 1695.
42. Nosé, S. J. Chem. Phys. 1984, 81, 511.
43. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187.
44. MacKerell, A. D., Jr.; et al. FASEB J. 1992, 6. A143.
45. MacKerell, A. D., Jr.; at al. Manuscript in preparation.
46. Ryckaert, J. P.; Ciccotti, G.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23, 327.
47. Shakhnovich, E. I.; Gutin, A. M. Nature 1990, 346, 773.
48. Ngo, J. T.; Karplus. M. J. Am. Chem. Soc. 1997, 119, 5657.
49. Némethy, G.; Pottle, M. S.; Scheraga, H. A. J. Phys. Chem. 1983, 87, 1883.
50. Sipple, M. J.; Némethy, G.; Scheraga, H. A. J. Phys. Chem. 1984, 88, 6231.
51. Koradi, R.; Billeter, M.; Wüthrich, K. J. Mol. Graphics 1996, 14, 51.