Dual-topology/dual-coordinate free-energy simulation using QM/MM force field

Journal of Chemical Physics

Volumn 123, Issue 4, 2005, Pages

  Hu, Hao ^a   Yang, Weitao ^a  

^a DUKE UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL PROCESSES; ENZYMATIC REACTIONS; FREE-ENERGY (FE) SIMULATION; MOLECULAR MECHANICS (MM);

COMPUTER SIMULATION; FREE ENERGY; MOLECULAR DYNAMICS; MONTE CARLO METHODS; PERTURBATION TECHNIQUES; THERMODYNAMICS; TOPOLOGY;

QUANTUM THEORY;

ARTICLE; CHEMICAL MODEL; COMPUTER SIMULATION; QUANTUM THEORY;

COMPUTER SIMULATION; MODELS, CHEMICAL; QUANTUM THEORY;

EID: 34548086475     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.1990113     Document Type: Article

References (41)

1. D. L. Beveridge and F. M. DiCapua, in Computer Simulation of Biomolecular Systems, edited by, W. F. van Gunsteren, and, P. K. Weiner, (ESCOM, Leiden, 1989), Vol. 1, p. 1.
2. W. F. van Gunsteren, in Computer Simulations of Biomolecular Systems, edited by, W. F. van Gunsteren, and, P. K. Weiner, (ESCOM, Leiden, The Netherlands, 1989), p. 27.
3. P. A. Kollman, Chem. Rev. (Washington, D.C.) 93, 2395 (1993).
4. T. Simonson, G. Archontis, and M. Karplus, Acc. Chem. Res. 35, 430 (2002).
5. W. L. Jorgensen, Science 303, 1813 (2004).
6. A. Shurki and A. Warshel, Adv. Protein Chem. 66, 249 (2003).
7. A. Warshel and M. Levitt, J. Mol. Biol. 103, 227 (1976).
8. U. C. Singh and P. A. Kollmann, J. Comput. Chem. 7, 718 (1986).
9. M. J. Field, P. A. Bash, and M. Karplus, J. Comput. Chem. 11, 700 (1990).
10. A. Warshel, Chem. Phys. Lett. 55, 454 (1978).
11. V. Th́ry, D. Rinaldi, J.-L. Rivail, B. Maigret, and G. G. Ferenczy, J. Comput. Chem. 15, 269 (1994).
12. Y. Zhang, T.-S. Lee, and W. Yang, J. Chem. Phys. 110, 46 (1999).
13. J. Chandrasekhar, S. F. Smith, and W. L. Jorgensen, J. Am. Chem. Soc. 107, 154 (1985).
14. J.-K. Hwang, G. King, S. Creighton, and A. Warshel, J. Am. Chem. Soc. 110, 5297 (1988).
15. Y. Zhang, H. Liu, and W. Yang, J. Chem. Phys. 112, 3483 (2000).
16. H. Liu and Y. Shi, J. Comput. Chem. 15, 1311 (1994).
17. Q. Cui, M. Elstner, and M. Karplus, J. Phys. Chem. B 106, 2721 (2002).
18. T. Wesolowski and A. Warshel, J. Phys. Chem. 98, 5183 (1994).
19. T. Wesolowski, R. P. Muller, and A. Warshel, J. Phys. Chem. 100, 15444 (1996).
20. R. P. Muller and A. Warshel, J. Phys. Chem. 99, 17516 (1995).
21. J. Bentzien, R. P. Muller, J. Florián, and A. Warshel, J. Phys. Chem. B 102, 2293 (1998).
22. V. Luzhkov and A. Warshel, J. Comput. Chem. 13, 199 (1992).
23. M. Strajbl, G. Hong, and A. Warshel, J. Phys. Chem. B 106, 13333 (2002).
24. R. H. Wood, E. M. Yezdimer, S. Sakane, J. A. Barriocanal, and D. J. Doren, J. Chem. Phys. 110, 1329 (1999).
25. S. Sakane, E. M. Yezdimer, W. Liu, J. A. Barriocanal, D. J. Doren, and R. H. Wood, J. Chem. Phys. 113, 2583 (2000).
26. G. Li, X. Zhang, and Q. Cui, J. Phys. Chem. B 107, 8643 (2003).
27. G. Li and Q. Cui, J. Phys. Chem. B 107, 14521 (2003).
28. W. Yang, R. Bitetti-Putzer, and M. Karplus, J. Chem. Phys. 120, 9450 (2004).
29. M. R. Reddy, U. C. Singh, and M. D. Erion, J. Am. Chem. Soc. 126, 6224 (2004).
30. D. Riccardi, G. Li, and Q. Cui, J. Phys. Chem. B 108, 6467 (2004).
31. G. Mann, R. H. Yun, L. Nyland, J. Prins, J. Board, and J. Hermans, in Computational Methods for Macromolecules: Challenges and Applications, Proceedings of the 3rd International Workshop on Algorithms for Macromolecular Modelling, edited by, T. Schlick, and, H. H. Gan, (Springer, New York, 2002), p. 129.
32. H. Hu, M. Elstner, and J. Hermans, Proteins: Struct., Funct., Genet. 50, 451 (2003).
33. M. Elstner, D. Porezag, G. Jungnickel, J. Elsner, M. Haugk, T. Frauenheim, S. Suhai, and G. Seifert, Phys. Rev. B 58, 7260 (1998).
34. M. Elstner, T. Frauenheim, E. Kaxiras, G. Seifert, and S. Suhai, Phys. Status Solidi B 217, 357 (2000).
35. W. L. Jorgensen, J. Chandrasekhar, J. D. Madura, R. W. Impey, and M. L. Klein, J. Chem. Phys. 79, 926 (1983).
36. A. D. MacKerell, Jr., D. Bashford, M. Bellott, R. L. Dunbrack, Jr., J. D. Evanseek, M. J. Field, S. Fischer, J. Gao, H. Guo, S. Ha, D. Joseph-McCarthy, L. Kuchnir, K. Kuczera, F. T. K. Lau, C. Mattos, S. Michnick, T. Ngo, D. T. Nguyen, B. Prodhom, W. E. Reiher, III, B. Roux, M. Schlenkrich, J. C. Smith, R. Stotc, J. Straub, M. Watanbe, J. Wiórkiewcz-Kuczera, D. Yin and M. Karplus, J. Phys. Chem. B 102, 3586 (1998).
37. J. Hermans, J. Phys. Chem. 95, 9029 (1991).
38. H. Hu, R. H. Yun, and J. Hermans, Mol. Simul. 28, 67 (2002).
39. S. Cabani, P. Gianni, V. Mollica, and L. Lepori, J. Solution Chem. 10, 563 (1981).
40. P. A. Kollman, Acc. Chem. Res. 29, 461 (1996).
41. J. Hermans and L. Wang, J. Am. Chem. Soc. 119, 2707 (1997).