A diffusion process-controlled Monte Carlo method for finding the global energy minimum of a polypeptide chain. I. Formulation and test on a hexadecapeptide

Journal of Chemical Physics

Volumn 106, Issue 12, 1997, Pages 5260-5270

  Derreumaux, Philippe ^a  

^a INST DE BIOLOGIE PHYSICO CHIMIQUE   (France)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0001170125     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.473525     Document Type: Article

References (49)

1. S. Vajda and C. Delisi, Biopolymers 29, 1755 (1990); M. H. Lambert and H. A. Scheraga, J. Comput. Chem. 10, 770 (1989).
2. S. Vajda and C. Delisi, Biopolymers 29, 1755 (1990); M. H. Lambert and H. A. Scheraga, J. Comput. Chem. 10, 770 (1989).
3. R. E. Bruccoleri, Mol. Sim. 10, 151 (1993).
4. S. Kirkpatrick, C. D. Gelatt, Jr., and M. P. Vecchi, Science 220, 671 (1983); S. R. Wilson and W. Cui, Biopolymers 29, 225 (1990).
5. S. Kirkpatrick, C. D. Gelatt, Jr., and M. P. Vecchi, Science 220, 671 (1983); S. R. Wilson and W. Cui, Biopolymers 29, 225 (1990).
6. R. E. Bruccoleri and M. Karplus, Biopolymers 26, 137 (1987).
7. G. M. Crippen, J. Comput. Chem. 3, 471 (1982).
8. E. O. Purisma and H. A. Scheraga, Proc. Natl. Acad. Sci. USA 83, 2782 (1986).
9. L. Piela, J. Kostrowski, and H. A. Scheraga, J. Phys. Chem. 93, 3339 (1989).
10. T. Head-Gordon and F. H. Stillinger, Biopolymers 33, 293 (1993).
11. R. Abagyan and M. Totrov, J. Mol. Biol. 235, 983 (1994).
12. J. Bascle, T. Garel, H. Orland, and B. Velikson, Biopolymers 33, 1843 (1993).
13. D. R. Ripoll and H. A. Sheraga, Biopolymers 27, 1283 (1988).
14. Z. Li and H. A. Scheraga, J. Mol. Struct. (Theochem) 179, 333 (1988).
15. N. S. Metropolis, A. W. Rosenbluth, M. N. Rosenbluth, A. H. Teller, and E. Teller, J. Chem. Phys. 21, 1087 (1953).
16. J. M. Scholtz, E. J. York, J. M. Stewart, and R. L. Baldwin, J. Am. Chem. Soc. 113, 5102 (1991).
17. N. D. Socci, J. N. Onuchic, and P. G. Wolynes, J. Chem. Phys. 104, 5860 (1996).
18. D. Bashford, C. Chothia, and A. M. Lesk, J. Mol. Biol. 196, 199 (1987).
19. W. F. DeGrado and J. D. Lear, J. Am. Chem. Soc. 107, 7684 (1985).
20. H. Xiong, B. L. Buckwalter, H-M Shieh, and M. H. Hecht, Proc. Natl. Acad. Sci. USA 92, 6349 (1995).
21. K. A. Dill, S. Bromberg, K. Yue, K. M. Fiebig, D. P. Yee, P. D. Thomas, and H. S. Chan, Protein Sci. 4, 561 (1995).
22. C. Wilson and S. Doniach, Proteins Struct. Funct. Genet. 6, 193 (1989).
23. M. Levitt, J. Mol. Biol. 104, 59 (1976).
24. A. Wallqvist and M. Ullner, Proteins Struct. Funct. Genet. 18, 267 (1994).
25. R. Srinivasan and G. D. Rose, Proteins Struct. Funct. Genet. 22, 81 (1995).
26. C. M. Wilmot and J. M. Thornton, J. Mol. Biol. 203, 221 (1988).
27. G. D. Rose, Adv. Protein Chem. 37, 1 (1985).
28. J. Novotny, R. Bruccoleri, and M. Karplus, J. Mol. Biol. 177, 787 (1984).
29. Y. Wang, H. Zhang, and R. A. Scott, Protein Sci. 4, 1402 (1995).
30. J. Israelachvili and R. Pashley, Nature 300, 341 (1982).
31. M. Gilson and B. Honig, Nature 330, 84 (1987).
32. S. J. Weiner, P. A. Kollman, D.A. Case, U. C. Singh, C. Ghio, G. Alagona, S. Profeta, and P. Weiner, J. Am. Chem. Soc. 106, 765 (1984).
33. M. Whitlow and M. M. Teeter, J. Am. Chem. Soc. 108, 7163 (1986).
34. D. J. E. Callaway Proteins Struct. Funct. Genet. 20, 124 (1994).
35. Protein Folding, edited by T. E. Creighton (W. H. Freeman, New York, 1993).
36. A. Sali, E. Shakhnovich, and M. Karplus, J. Mol. Biol. 235, 1614 (1994).
37. J. D. Bryngelson and P. G. Wolynes, Proc. Natl. Acad. Sci. USA 84, 7524 (1987).
38. M-H. Hao and H. A. Scheraga, J. Phys. Chem. 98, 4940 (1994).
39. N. G. Van Kampen, in Stochastic Processes in Physics and Chemistry (Elsevier, The Netherlands, 1992).
40. R. Zwanzig, J. Chem. Phys. 79, 4507 (1983).
41. B. Madan, T. Keeyes, and G. Seeley, J. Chem. Phys. 92, 7565 (1989).
42. R. Czerminski and R. Elber, J. Chem. Phys. 92, 5580 (1990).
43. V. Daggett, P. Kollman, and I. D. Kuntz, Biopolymers 31, 1115 (1991).
44. P. Derreumaux, G. Zhang, B. R. Brooks, and T. Schlick, J. Comput. Chera. 15, 532 (1994).
45. E. K. Bradley, J. F. Thomson, F. E. Cohen, P. A. Kosen, and I. D. Kuntz, J. Mol. Biol. 215, 607 (1990).
46. S. S. Sung, and X. W. Wu, Proteins Struct. Funct. Genet. 25, 202 (1996).
47. C. L. Brooks, III and D. A. Case, Chem. Rev. 93, 2487 (1993).
48. P. Derreumaux and R. Lavery (in preparation).
49. K. R. Shoemaker, P. S. Kim, D. N. Brems, S. Marqusee, E. J. York, I. M. Chaiken, J. M. Stewart, and R. L. Baldwin, Proc. Natl. Acad. Sci. USA 82, 2349 (1985).