Efficiency of Monte Carlo minimization procedures and their use in analysis of NMR data obtained from flexible peptides

Journal of Computational Chemistry

Volumn 18, Issue 2, 1997, Pages 240-253

  Meirovitch, Hagai ^a   Meirovitch, Eva ^a  

^a FLORIDA STATE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0001442134     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/(SICI)1096-987X(19970130)18:2<240::AID-JCC8>3.0.CO;2-V     Document Type: Article

References (59)

1. H. A. Scheraga, In Reviews in Computational Chemistry, Vol. 3, K. D. Lipkowitz and D. B. Boyd, Eds, VCH Publishers, New York, 1992, p. 73.
2. M. Karplus and G. A. Petsko, Nature, 347, 631 (1990).
3. M. Vásquez, E. Meirovitch, and H. Meirovitch, J. Phys. Chem., 98, 9380 (1994).
4. H. Meirovitch, E. Meirovitch, and J. Lee, J. Phys. Chem., 99, 4847 (1995).
5. E. Meirovitch and H. Meirovitch, Biopolymers, 38, 69 (1996).
6. (a) H. Kessler, C. Griesinger, J. Lautz, A. Muller, W. F. van Gunsteren, and H. J. C. Berendsen, J. Am. Chem. Soc., 110, 3393 (1988)
7. (b) D. F. Mierke, R. M. Scheek, and H. Kessler, Biopolymers, 34, 559 (1994)
8. (c) J. Yang and T. F. Havel, J. Biomol. NMR, 3, 355 (1993)
9. (d) R. Brüschweiler, M. Blackledge, and R. R. Ernst, J. Biomol. NMR, 1, 3 (1991)
10. (e) M. J. Blackledge, R. Brüschweiler, C. Griesinger, J. M. Schmidt, P. Xu, and R. R. Ernst, Biochemistry, 32, 10960 (1993)
11. (f) G. V. Nikiforovich, O. Prakash, C. A. Gehrig, and V. J. Hruby, J. Am. Chem. Soc., 115, 3399 (1993)
12. (g) C. Landis and V. S. Allured, J. Am. Chem. Soc., 113, 9493 (1991)
13. (h) D. O. Cicero, G. Barbato, and R. Bazzo, J. Am. Chem. Soc., 117, 1027 (1995).
14. (a) M. Saunders, K. N. Houk, Y. D. Wu, W. C. Still, M. Lipton, G. Chang, and W. C. Guida, J. Am. Chem. Soc., 112, 1419 (1990)
15. (b) N. Weinberg and S. Wolfe, J. Am. Chem. Soc., 116, 9860 (1994)
16. (c) R. A. Abagyan and P. Argos, J. Mol. Biol., 225, 519 (1992).
17. N. Metropolis, A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller, and E. Teller, J. Chem. Phys., 21, 1087 (1953).
18. (a) B. J. Alder and T. E. Wainwright, J. Chem. Phys., 31, 459 (1959)
19. (b) J. A. McCammon, B. R. Gelin, and M. Karplus, Nature, 267, 585 (1977).
20. (a) Z. Li and H. A. Scheraga, Proc. Natl. Acad. Sci. USA, 84, 6611 (1987)
21. (b) J. Mol. Struct. (Theochem.), 179, 333 (1988).
22. (a) M. Saunders, J. Am. Chem. Soc., 109, 3150 (1987)
23. (b) D. M. Ferguson and D. J. Raber, J. Am. Chem. Soc., 111, 4371 (1989)
24. (c) G. Chang, W. C. Guida, and W. C Still, J. Am. Chem. Soc., 111, 4379 (1989)
25. (d) H. Meirovitch, J. Phys. A, 15, L735 (1982)
26. (e) H. Meirovitch, M. Vásquez, and H. A. Scheraga, J. Chem. Phys., 92, 1248 (1990).
27. (a) U. H. E. Hansmann and Y. Okamoto, J. Comp. Chem., 14, 1333 (1993)
28. (b) B. A. Berg and T. Neuhaus, Phys. Lett. B, 267, 249 (1991).
29. (a) S. R. Wilson, W. Cui, J. W. Moskowitz, and K. E. Schmidt, Tetrahedron Lett., 29, 4373 (1988)
30. (b) S. Kirkpatrick, C. D. Gelatt, and M. P. Vecchi, Science, 220, 671 (1983).
31. R. C. Schaik, W. F. van Gunsteren, and H. J. C. Berendsen, J. Comput.-Aided Mol. Design, 6, 97 (1992).
32. M. Vásquez, G. Némethy, and H. A. Scheraga, Chem. Rev., 94, 2183 (1994).
33. (a) F. A. Momany, R. F. McGuire, A. W. Burgess, and H. A. Scheraga, J. Phys. Chem., 79, 2361 (1975)
34. (b) G. Némethy, M. S. Pottle, and H. A. Scheraga, J. Phys. Chem., 87, 1833 (1983)
35. (c) M. J. Sippl, G. Némethy, and H. A. Scheraga, J. Phys. Chem., 88, 6231 (1984).
36. H. Meirovitch and E. Meirovitch, J. Phys. Chem., 100, 5123 (1996).
37. (a) F. H. Stillinger and T. A. Weber, J. Phys. Chem., 87, 2833 (1983)
38. (b) F. H. Stillinger and T. A. Weber, Science, 225, 983 (1984)
39. (c) R. Elber and M. Karplus, Science, 235, 318 (1987).
40. A. Caflisch, P. Niederer, and M. Anliker, Proteins: Struct. Funct. Genet., 14, 102 (1992).
41. A. Nayeem, J. Vila, and H. A. Scheraga, J. Compt. Chem., 12, 594 (1991).
42. B. von Freyberg and W. Braun, J. Comp. Chem., 12, 1065 (1991).
43. D. R. Ripoll and H. A. Scheraga, J. Protein Chem., 8, 263 (1989).
44. (a) N. Gō and H. A. Scheraga, J. Chem. Phys., 51, 4751 (1969)
45. (b) K. D. Gibson and H. A. Scheraga, Physiol. Chem. Phys., 1, 109 (1969)
46. (c) N. Go and H. A. Scheraga, Macromolecules, 9, 535 (1976).
47. A. T. Hagler, P. S. Stern, R. Sharon, J. M. Becker, and F. Naider, J. Am. Chem. Soc., 101, 6842 (1979).
48. (a) M. Karplus and J. N. Kushick, Macromolecules, 14, 325 (1981)
49. (b) D. A. Case, Curr. Opin. Struct. Biol., 4, 285 (1994).
50. (a) H. Meirovitch, E. Meirovitch, A. G. Michel, and M. Vásquez, J. Phys. Chem., 98, 6241 (1994)
51. (b) H. Meirovitch and H. A. Scheraga, Macromolecules, 14, 1250 (1981).
52. (a) H. Meirovitch, Chem. Phys. Lett., 21, 389 (1977)
53. (b) H. Meirovitch, M. Vásquez, and H. A. Scheraga, Biopolymers, 26, 651 (1987)
54. (c) H. Meirovitch, D. H. Kitson, and A. T. Hagler, J. Am. Chem. Soc., 114, 5386 (1992)
55. (d) H. Meirovitch, S. C. Koerber, J. Rivier, and A. T. Hagler, Biopolymers, 34, 815 (1994).
56. (a) T. Schaumann, W. Braun, and K. Wüthrich, Biopolymers, 29, 679 (1990)
57. (b) B. von Freyberg and W. Braun, J. Comp. Chem., 14, 510 (1993)
58. (c) B. von Freyberg, T. J. Richmond, and W. Braun, J. mol. Biol., 233, 275 (1993)
59. (d) B. von Freyberg, T. Schaumann, and W. Braun, FANTOM User's Manual and Instructions, ETH Zürich, Zürich, 1993.