Alchemical free energy calculations and multiple conformational substates

Journal of Chemical Physics

Volumn 122, Issue 8, 2005, Pages

  Leitgeb, Martin ^a   Schröder, Christian ^a   Boresch, Stefan ^a  

^a UNIVERSITY OF VIENNA   (Austria)

Author keywords

[No Author keywords available]

Indexed keywords

ALCHEMICAL FREE ENERGY SIMULATIONS; ATOMIC MODELS; PARTITION FUNCTIONS; THERMODYNAMIC INTEGRATION (TI);

COMPUTATIONAL METHODS; COMPUTER SIMULATION; CONFORMATIONS; CONVERGENCE OF NUMERICAL METHODS; FUNCTIONS; MATHEMATICAL MODELS; SUBSTRATES; THERMODYNAMICS;

FREE ENERGY;

EID: 22944450355     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.1850900     Document Type: Article

References (74)

1. P. Kollman, Chem. Rev. (Washington, D.C.) 93, 2395 (1993).
2. T. Simonson, G. Archontis, and M. Karplus, Acc. Chem. Res. 35, 430 (2002).
3. P. A. Kollman, Acc. Chem. Res. 29, 461 (1996).
4. T.P. Straatsma, in Reviews in Computational Chemistry, edited by, K. B. Lipkowitz, and, D. B. Boyd, (VCH, New York, 1996), Vol. 9, pp. 81-127.
5. R. H. Henchman and J. W. Essex, J. Comput. Phys. 20, 499 (1998).
6. J. L. Miller and P. A. Kollman, J. Phys. Chem. 100, 8587 (1996).
7. F. T. K. Lau and M. Karplus, J. Mol. Biol. 236, 1049 (1994).
8. M. L. Lamb and W. L. Jorgensen, J. Med. Chem. 41, 3928 (1998).
9. G. Archontis, T. Simonson, and M. Karplus, J. Mol. Biol. 306, 307 (2001).
10. T. Koichi and K. Shimizu, J. Phys. Chem. B 102, 6419 (1998).
11. T. C. Beutler, A. E. Mark, R. C. van Schaik, P. R. Gerber, and W. F. van Gunsteren, Chem. Phys. Lett. 222, 529 (1994).
12. M. Zacharias, T. P. Straatsma, and J. A. McCammon, J. Phys. Chem. 100, 9025 (1994).
13. T. Simonson, Mol. Phys. 80, 441 (1993).
14. S. Boresch and M. Karplus, J. Phys. Chem. A 103, 103 (1999).
15. S. Shobana, B. Roux, and O. S. Andersen, J. Phys. Chem. B 104, 5179 (2000).
16. S. Boresch, Mol. Simul. 28, 13 (2002).
17. T. Simonson, G. Archontis, and M. Karplus, J. Phys. Chem. B 101, 8349 (1997).
18. W. Im, S. Bernèche, and B. Roux, J. Chem. Phys. 114, 2924 (2000).
19. T. Simonson, J. Phys. Chem. B 104, 6509 (2000).
20. M. K. Gilson, J. A. Given, B. L. Bush, and J. A. McCammon, Biophys. J. 72, 1047 (1997).
21. S. Boresch, F. Tettinger, M. Leitgeb, and M. Karplus, J. Phys. Chem. B 107, 9535 (2003).
22. M. Shirts and V. S. Pande, Science 290, 1903 (2000).
23. M. R. Shirts, J. W. Pitera, W. C. Swope, and V. S. Pande, J. Chem. Phys. 119, 5740 (2003).
24. Y. Deng and B. Roux, J. Phys. Chem. B 108, 16567 (2004).
25. G. Kaminski, E. M. Duffy, T. Matsui, and W. L. Jorgensen, J. Phys. Chem. 98, 13077 (1994).
26. A. Villa, R. Zangi, G. Pieffet, and A. E. Mark, J. Comput.-Aided Mol. Des. 17, 673 (2003).
27. J. Sarzynska, L. Nilsson, and T. Kulinski, Biophys. J. 85, 3445 (2003).
28. D. L. Beveridge and F. M. DiCapua, Annu. Rev. Biophys. Biophys. Chem. 18, 431 (1989).
29. W. Yang, R. Bitetti-Putzer, and M. Karplus, J. Chem. Phys. 120, 2618 (2004).
30. S. Boresch, M. Leitgeb, A. Beselman, and A.D. MacKerell (unpublished).
31. R. Bitetti-Putzer, W. Yang, and M. Karplus, Chem. Phys. Lett. 377, 633 (2003).
32. D. J. Tobias, C. L. Brooks III, and S. H. Fleischman, Chem. Phys. Lett. 156, 256 (1989).
33. T. P. Straatsma and J. A. McCammon, J. Chem. Phys. 90, 3300 (1989).
34. T. P. Straatsma and J. A. McCammon, J. Chem. Phys. 91, 3631 (1989).
35. J. Hermans, R. H. Yun, and A. G. Anderson, J. Comput. Phys. 13, 429 (1992).
36. T. P. Straatsma and J. A. McCammon, J. Chem. Phys. 101, 5032 (1994).
37. N. Ota and A. T. Brünger, Theor. Chem. Acc. 98, 171 (1997).
38. A. Hodel, L. M. Rice, T. Simonson, R. O. Fox, and A. T. Brünger, Protein Sci. 4, 636 (1995).
39. H. Grubmüller, Phys. Rev. E 52, 2893 (1995).
40. Y. Sugita and Y. Okamoto, Chem. Phys. Lett. 314, 141 (1999).
41. X. Wu and B. R. Brooks, Chem. Phys. Lett. 381, 512 (2003).
42. D. Hamelberg, J. Mongan, and J. A. McCammon, J. Chem. Phys. 120, 11919 (2004).
43. U. H. E. Hansmann, Chem. Phys. Lett. 281, 140 (1997).
44. Y. Sugita, A. Kitao, and Y. Okamoto, J. Chem. Phys. 113, 6042 (2000).
45. B. A. Berg and T. Neuhaus, Phys. Lett. B 267, 249 (1991).
46. U. H. E. Hansmann, Y. Okamoto, and F. Eisenmenger, Chem. Phys. Lett. 259, 321 (1996).
47. C. Simmerling, T. Fox, and P. A. Kollman, J. Am. Chem. Soc. 120, 5771 (1998).
48. C. J. Woods, J. W. Essex, and M. A. King, J. Phys. Chem. B 107, 13703 (2003).
49. C. J. Woods, J. W. Essex, and M. A. King, J. Phys. Chem. B 107, 13711 (2003).
50. C. J. Wood, S. Camiolo, M. E. Light, S. J. Coles, M. B. Hursthouse, M. A. King, P. A. Gale, and J. W. Essex, J. Am. Chem. Soc. 124, 8644 (2002).
51. X. Kong and C. L. Brooks III, J. Chem. Phys. 105, 2414 (1996).
52. M. Souaille and B. Roux, Comput. Phys. Commun. 135, 40 (2001).
53. C. Bartels and M. Karplus, J. Comput. Phys. 18, 1450 (1997).
54. M. Mezei and D. L. Beveridge, Ann. N.Y. Acad. Sci. 1, 1 (1986).
55. D.L. Beveridge and F.M. DiCapua, in Computer Simulation of Biomolecular Systems, edited by, W. F. van Gunsteren, and, P. K. Weiner, (ESCOM Science, Leiden, 1989), pp. 1-26.
56. S. Kumar, D. Bouzida, R. H. Swendsen, P. A. Kollman, and J. M. Rosenberg, J. Comput. Phys. 13, 1011 (1992).
57. G. M. Torrie and J. P. Valleau, J. Comput. Phys. 23, 187 (1977).
58. B. R. Brooks, R. E. Bruccoleri, B. D. Olafson, D. J. States, S. Swaminathan, and M. Karplus, J. Comput. Phys. 4, 187 (1983).
59. D. R. Herschbach, H. S. Johnston, and D. Rapp, J. Chem. Phys. 31, 1652 (1959).
60. S. Boresch and M. Karplus, J. Phys. Chem. A 103, 119 (1999).
61. K.S. Pitzer, Quantum Chemistry (Prentice-Hall, Englewood Cliffs, NJ, 1987).
62. C. Bartels and M. Karplus, J. Phys. Chem. B 102, 865 (1998).
63. Wolfram Research, Inc., MATHEMATICA, Version 4.0, Champaign, IL, (1999).
64. R. Wolfenden, L. Andersson, P. M. Cullis, and C. C. B. Southgate, Biochemistry 20, 849 (1981).
65. A. D. MacKerell, Jr., D. Bashford, M. Bellott et al., J. Phys. Chem. B 102, 3586 (1998).
66. W. L. Jorgensen, J. Chandrasekhar, and J. D. Madura, J. Chem. Phys. 79, 926 (1983).
67. E. Neria, S. Fischer, and M. Karplus, J. Chem. Phys. 105, 1902 (1996).
68. J. P. Ryckaert, G. Ciccotti, and H. J. C. Berendsen, J. Comput. Phys. 23, 327 (1977).
69. W. G. Hoover, Phys. Rev. A 31, 1695 (1985).
70. B. L. Tembe and J. A. McCammon, Comput. Chem. (Oxford) 8, 281 (1984).
71. D. A. Pearlman and P. A. Kollman, J. Chem. Phys. 94, 4532 (1991).
72. M. Prévost, S. J. Wodak, B. Tidor, and M. Karplus, Proc. Natl. Acad. Sci. U.S.A. 88, 10880 (1991).
73. M. Leitgeb (unpublished).
74. R. D. Woods and D. S. Saxon, Phys. Rev. 95, 577 (1954).