The development of replica-exchange-based free-energy methods

Journal of Physical Chemistry B

Volumn 107, Issue 49, 2003, Pages 13703-13710

  Woods, Christopher J ^a   Essex, Jonathan W ^a   King, Michael A ^b  

^a UNIVERSITY OF SOUTHAMPTON   (United Kingdom)

^b UCB PHARMA   (Belgium)

Author keywords

[No Author keywords available]

Indexed keywords

FINITE DIFFERENCE METHOD; HYDRATION; MATHEMATICAL MODELS; METHANE; PERTURBATION TECHNIQUES; THERMODYNAMICS; WATER;

FINITE DIFFERENCE THERMODYNAMIC INTEGRATION; FREE ENERGY PERTURBATION; REPLICA EXCHANGE METHOD;

FREE ENERGY;

EID: 0346350789     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp0356620     Document Type: Article

References (45)

1. Sugita, Y.; Kitao, A.; Okamoto, Y. J. Chem. Phys. 2000, 113, 6042-6051.
2. Fukunishi, H.; Watanabe, O.; Takada, S. J. Chem. Phys. 2002, 116, 9058-9067.
3. Hansmann, U. H. E. Chem. Phys. Lett. 1997, 281, 140-150.
4. Sugita, Y.; Okamoto, Y. Chem. Phys. Lett. 1999, 314, 141-151.
5. Sanbonmatsu, K. Y.; Garcia, A. E. Proteins 2002, 46, 225-234.
6. Zhou, R. H.; Berne, B. J. Proc. Natl. Acad. Sci. 2002, 99, 12777-12782.
7. Verkhivker, G. M.; Rejto, P. A.; Bouzida, D.; Arthurs, S.; Colson, A. B.; Freer, S. T.; Gehlhaar, D. K.; Larson, V.; Luty, B. A.; Marrone, T.; Rose, P. W. Chem. Phys. Lett. 2001, 337, 181-189.
8. Zwanzig, R. W. J. Chem. Phys. 1954, 22, 1420-1426.
9. Price, M. L. P.; Jorgensen, W. L. J. Am. Chem. Soc. 2000, 122, 9455-9466.
10. Price, D. J.; Jorgensen, W. L. Bioorg. Med. Chem. Lett. 2000, 10, 2067-2070.
11. Price, D. J.; Jorgensen, W. L. J. Comput. Aid. Mol. Des. 2001, 15, 681-695.
12. Pearlman, D. A.; Charifson, P. S. J. Med. Chem. 2001, 44, 3417-3423.
13. Oostenbrink, B. C.; Pitera, J. W.; Lipzig, M. M. H.; Meerman, J. H. N.; Van Gunsteren, W. F. J. Med. Chem. 2000, 43, 4594-4605.
14. Barril, X.; Orozco, M.; Luque, F. J. J. Med. Chem. 1999, 42, 5110-5119.
15. Torrie, G. M.; Valleau, J. P. J. Comput. Phys. 1977, 23, 187-199.
16. Hooft, R. W. W.; Vaneijck, B. P.; Kroon, J. J. Chem. Phys. 1992, 97, 6690-6694.
17. Engkvist, O.; Karlstrom, G. Chem. Phys. 1996, 213, 63-76.
18. Bartels, C.; Karplus, M. J. Comput. Chem. 1997, 18, 1450-1462.
19. Kumar, S.; Payne, P. W.; Vasquez, M. J. Comput. Chem. 1996, 17, 1269-1275.
20. Reynolds, C. A.; King, P. M.; Richards, W. G. Mol. Phys. 1992, 76, 251-275.
21. Chipot, C.; Pearlman, D. A. Mol. Simulat. 2002, 28, 1-12.
22. Jarzynski, C. Phys. Rev. E 1997, 56, 5018-5035.
23. Jarzynski, C. Phys. Rev. Lett. 1997, 78, 2690-2693.
24. Jarzynski, C. Proc. Natl. Acad. Sci. 2001, 98, 3636-3638.
25. Hummer, G. J. Chem. Phys. 2001, 114, 7330-7337.
26. Wood, R. H.; Muhlbauer, W. C. F.; Thompson, P. T. J. Phys. Chem. 1991, 95, 6670-6675.
27. Jorgensen, W. L.; Ravimohan, C. J. Chem. Phys. 1985, 83, 3050-3054.
28. Mezei, M. J. Chem. Phys. 1987, 86, 7084-7088.
29. Guimaraes, C. R. W.; Alencastro, R. B. Int. J. Quantum Chem. 2001, 85, 713-726.
30. Guimaraes, C. R. W.; Alencastro, R. B. J. Med. Chem. 2002, 45, 4995-5004.
31. Guimaraes, C. R. W.; Alencastro, R. B. J. Phys. Chem. B 2002, 106, 466-476.
32. Kamath, S.; Coutinho, E.; Desai, P. J. Biomol. Struct. Dyn. 1999, 16, 1239-1244.
33. Woodsm, C. J.; Camiolo, S.; Light, M. E.; Coles, S. J.; Hursthouse, M. B.; King, M. A.; Gale, P. A.; Essex, J. W. J. Am. Chem. Soc. 2002, 124, 8644-8652.
34. Kumar, S.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A.; Rosenberg, J. M. J. Comput. Chem. 1992, 13, 1011-1021.
35. Okabe, T.; Kawata, M.; Okamoto, Y.; Mikami, M. Chem. Phys. Lett. 2001, 335, 435-439.
36. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926-935.
37. Jorgensen, W. L.; Madura, J. D.; Swenson, C. J. J. Am. Chem. Soc. 1984, 106, 6638-6646.
38. Zhu, T. H.; Li, J. B.; Hawkins, G. D.; Cramer, C. J.; Truhlar, D. G. J. Chem. Phys. 1998, 109, 9117-9133.
39. Pearlman, D. A. J. Phys. Chem. 1994, 98, 1487-1493.
40. Owicki, J. C.; Scheraga, H. A. Chem. Phys. Lett. 1977, 47, 600-602.
41. Jorgensen, W. L. J. Phys. Chem. 1983, 87, 5304-5314.
42. Jorgensen, W. L. MCPRO, Version 1.5; Yale University: New Haven, CT, 1996.
43. Hernandez-Cobos, J.; Mackie, A. D.; Vega, L. F. J. Chem. Phys. 2001, 114, 7527-7535.
44. Dejong, P. H. K.; Wilson, J. E.; Neilson, G. W.; Buckingham, A. D. Mol. Phys. 1997, 91, 99-103.
45. Head-Gordon, T.; Hura, G. Chem. Rev. 2002, 102, 2651-2669.