Analysis and application of potential energy smoothing and search methods for global optimization

Journal of Physical Chemistry B

Volumn 102, Issue 48, 1998, Pages 9725-9742

  Pappu, Rohit V ^a   Hart, Reece K ^a   Ponder, Jay W ^a  

^a WASHINGTON UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0038424321     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp982255t     Document Type: Article

References (73)

1. Leach, A. R. Rev. Comput. Chem. 1991, 2, 1.
2. Scheraga, H. A. Rev. Comput. Chem. 1992, 3, 73.
3. Horst, R.; Tuy, H. J. Opt. Theor. Appl. 1987, 54, 253.
4. Némethy, G.; Scheraga, H. A. Biopolymers 1965, 3, 155.
5. Griewank, A. O. J. Opt. Theor. Appl. 1981, 34, 11.
6. Törn, A.; Zilinskas, A. Zilinskas, A. Global Optimization; Lecture Notes in Computer Science, Vol. 350; Springer-Verlag, Berlin, 1989; pp 117-151.
7. Kirkpatrick, S.; Gelatt, C. D.; Vecchi, M. P. Science 1983, 220, 671.
8. Metropolis, N.; Rosenbluth, A. W.; Rosenbluth, M. N.; Teller, A. H.; Teller, E. J. J. Chem. Phys. 1953, 21, 1087.
9. Berg, B. A.; Neuhaus, T. Phys. Lett. B 1991, 267, 249.
10. Li, Z.; Scheraga, H. A. Proc. Natl. Acad. Sci. U.S.A. 1987, 84, 6611.
11. Wales, D. J.; Doye, J. P. K. J. Phys. Chem. A 1997, 101, 5111.
12. Li, Z.; Laidig, K. E.; Daggett, V. J. Comput. Chem. 1998, 19, 60.
13. Guarnieri, F.; Still, W. C. J. Comput. Chem. 1994, 75, 1302.
14. Saunders, M. J. Comput. Chem. 1989, 10, 203.
15. Brünger, A. T.; Kuriyan, J.; Karplus, M. Science 1987, 235, 458.
16. van Laarhoven, P. J. M.; Aarts, E. H. L. Simulated Annealing: Theory and Applications; Kluwer Academic Publishers: Amsterdam, 1987.
17. Straub, J. E. In Recent Developments in Theoretical Studies of Proteins; Elber, R. E., Ed.; World Scientific: Singapore, 1996; p 137.
18. Wilson, S. R.; Cui, W. Biopolymers 1990, 29, 225.
19. Brünger, A. T.; Rice, L. M. Methods Enzymol. 1997, 277, 243.
20. Ingber, L. Math. Comput. Model 1989, 12, 967.
21. Wang, Z.; Pachter, R. J. Comput. Chem. 1997, 18, 323.
22. Tsallis, C. J. Stat. Phys. 1988, 52, 479.
23. Tsallis, C.; Stariolo, D. A. Physica A 1996, 233, 395.
24. Andricioaei, I.; Straub, J. E. Phys. Rev. E 1996, 53, R3055.
25. Simon, I.; Némethy, G.; Scheraga, H. A. Macromolecules 1978, 11, 797.
26. Pincus, M. R.; Klausner, R. D.; Scheraga, H. A. Proc. Natl. Acad. Sci. U.S.A. 1982, 79, 5107.
27. Dammkoehler, R. A.; Karasek, S. F.; Shands, E. F. B.; Marshall, G. R. J. Comput.-Aid. Mol. Des. 1989, 3, 3.
28. Merovitch, H.; Vasquez, M.; Scheraga, H. A. J. Chem. Phys. 1990, 92, 1248.
29. Goldberg, D. E. Genetic Algorithms in Search, Optimization, and Machine Learning; Addison-Wesley: Reading, MA, 1989.
30. Hoare, M. R.; McInnes, J. A. Adv. Phys. 1983, 32, 791.
31. Stillinger, F. H.; Weber, T. J. Stat. Phys. 1988, 52, 1429.
32. Piela, L.; Kostrowicki, J.; Scheraga, H. A. J. Phys. Chem. 1989, 93, 3339.
33. Ma, J.; Straub, J. E. J. Chem. Phys. 1993, 101, 533.
34. Amara, P.; Straub, J. E. Phys. Rev., B 1996, 53, 13857.
35. Ma, J.; Hsu, D.; Straub, J. E. J. Chem. Phys. 1993, 99, 4024.
36. Shalloway, D. In Recent Advances in Global Optimization; Floudas, C. A., Pardalos, P. M., Eds.; Princeton University Press: Princeton, NJ, 1992; pp 433.
37. Church, B.; Oresic, M.; Shalloway, D. In Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding; DIMACS, Vol. 23; Pardalos, P. M., Shalloway, D., Xue, G., Eds.; Am. Math. Soc.: Providence, RI, 1996; p 41.
38. Nakamura, S.; Hirose, H.; Ikeguchi, M.; Doi, J. J. Phys. Chem. 1995, 99, 8374.
39. Ponder, J. W. TINKER: Software Tools for Molecular Design, Version 3.6; Washington University School of Medicine, 1998.
40. Weiner, S. J.; Kollman, P. A.; Case, D. A.; Singh, U. C.; Ghio, C.; Alagona, G.; Profeta, S., Jr.; Weiner, P. J. Am. Chem. Soc. 1984, 106, 765.
41. Jorgensen, W. L.; Tirado-Rives, J. J. Am. Chem. Soc. 1988, 110, 1657.
42. Allinger, N. L. J. Am. Chem. Soc. 1977, 99, 8127.
43. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187.
44. Moré, J.; Wu, Z. In Global Minimization of Nonconvex Energy Functions: Molecular Conformation and Protein Folding; DIMACS, Vol. 23; Pardalos, P. M., Shalloway, D., Xue, G., Eds.; Am. Math. Soc.: Providence, RI, 1996; p 151.
45. Kostrowicki, J.; Piela, L.; Cherayil, B. J.; Scheraga, H. A. J. Phys. Chem. 1991, 95, 4113.
46. Kostrowicki, J.; Scheraga, H. A. J. Phys. Chem. 1992, 96, 7442.
47. Amara, P.; Straub, J. E. J. Phys. Chem. 1995, 99, 14840.
48. Davidon, W. C. Math. Programming 1975, 9, 1.
49. Ponder, J. W.; Richards, F. M. J. Comput. Chem. 1987, 8, 1016.
50. Czerminski, R.; Elber, R. J. Chem. Phys. 1990, 92, 5580.
51. Ulitsky, A.; Shalloway, D. J. Chem. Phys. 1997, 106, 10099.
52. Cerjan, C. J.; Miller, W. H. J. Chem. Phys. 1981, 75, 2800.
53. Barkema, G. T.; Mousseau, N. Phys. Rev. Lett. 1996, 77, 4358.
54. Northby, J. A. J. Chem. Phys. 1987, 6, 599.
55. Tsoo, C.; Brooks III, C. L. J. Chem. Phys. 1994, 101, 6405.
56. Doye, J. P. K.; Wales, D. J. Phys. Rev. Lett. 1998, 80, 1357.
57. Pillardy, J.; Piela, L. J. Phys. Chem. 1995, 99, 11805.
58. Zimmerman, S. S.; Pottle, M. S.; Némethy, G.; Scheraga, H. A. Macromolecules 1977, 10, 1.
59. Hart, R. K.; Pappu, R. V.; Ponder, J. W., to be submitted for publication.
60. Saunders, M.; Houk, K. N.; Wu, Y.D.; Still, W. C.; Lipton, M.; Chang, G.; Guida, W. C. J. Am. Chem. Soc. 1990, 112, 1419.
61. Ngo, J. T.; Karplus, M. J. Am. Chem. Soc. 1997, 119, 5657.
62. Chou, K. C.; Némethy, G.; Scheraga, H. A. J. Am. Chem. Soc. 1984, 106, 3161.
63. Crick, F. Acta Crystallogr. 1953, 6, 689.
64. Chothia, C.; Levitt, M.; Richardson, D. J. Mol. Biol. 1981, 145, 215.
65. Walther, D.; Eisenhaber, F.; Argos, P. J. Mol. Biol. 1996, 255, 536.
66. Goldstein, H. Classical Mechanics; Addison-Wesley: Reading, MA, 1980; Chapter 4 and Appendix B.
67. Huber, T.; Torda, A. E.; van Gunsteren, W. F. J. Phys. Chem. A 1997, 101, 5926.
68. Smellie, A.; Teig, S. L.; Towbin, P. J. Comput. Chem. 1995, 16, 17.
69. Roitberg, A.; Elber, R. J. Chem. Phys. 1991, 95, 9277.
70. Wawak, R. J.; Gibson, K. D.; Liwo, A.; Scheraga, H. A. Proc. Natl. Acad. Sci., U.S.A. 1996, 93, 1743.
71. Wawak, R. J.; Pillardy, J.; Liwo, A.; Gibson, K. D.; Scheraga, H. A. J. Phys. Chem. A 1998, 102, 2904.
72. Pillardy, J.; Piela, L. J. Comput. Chem. 1997, 18, 2040.
73. Moré, J.; Wu, Z. In Large Scale Optimization with Applications: Molecular Structure and Optimization, Biegler, L. T., Coleman, T. F., Conn, A. R., Santosa, F. N., Eds.; Springer- Verlag: New York, 1997; p 99.