Efficient and flexible algorithm for free energy calculations using the λ-dynamics approach

Journal of Physical Chemistry B

Volumn 102, Issue 11, 1998, Pages 2032-2036

  Guo, Z ^a   Brooks III, C L ^a   Kong, X ^b  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

^b ACCELRYS INC   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0000381173     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp972699+     Document Type: Article

References (30)

1. Tobias, D. J.; Sneddon, S. F.; Brooks, C. L., III. J. Mol. Biol. 1992, 227, 1244-1252.
2. Tobias, D. J.; Sneddon, S. F.; Brooks, C. L., III. J. Mol. Biol. 1990, 216, 783-796.
3. Sneddon, S. F.; Tobias, D. J.; Brooks, C. L., III. J. Mol. Biol. 1989, 209, 817-820.
4. Jorgensen, W. L.; Ravimohan, C. J. Chem. Phys. 1985, 83, 3050.
5. Bash, P.; Chandra, S.; Brown, F. K.; Langridge, R.; Kollman, P. A. Science 1987, 235, 574-576.
6. Bash, P. A.; Singh, U. C.; Langridge, R.; Kollman, P. A. Science 1987, 236, 564-568.
7. McDonald, J. J.; Brooks, C. L., III. J. Am. Chem. Soc. 1991, 113, 2295-2301.
8. McDonald, J. J.; Brooks, C. L., III. J. Am. Chem. Soc. 1992, 114, 2062-2072.
9. Zwanzig, R. W. J. Chem. Phys. 1954, 22, 1420.
10. Straatsma, T. P.; McCammon, J. A. Annu. Rev. Phys. Chem. 1992, 43, 407-435.
11. Beveridge, D. L.; DiCapua, F. M. Annu. Rev. Biophys. Biophys. Chem. 1989, 92, 18-431.
12. Brooks, C. L., III; Karplus, M.; Pettitt, B. N. Proteins: A Theoretical Perspective of Dynamics, Structure, and Thermodynamics.; John Wiley & Sons: New York, 1988.
13. Hansson, T.; Aqvist, J. Protein Eng. 1995, 8, 1137-1144.
14. Jones-Hertzog, D. K.; Jorgensen, W. L. J. Med. Chem. 1997, 40, 1539-1549.
15. Kong, X.; Brooks, C. L., III. J. Chem. Phys. 1996, 105, 2414-2423.
16. Verkhivker, G.; Elber, R.; Nowak, W. J. Chem. Phys. 1992, 97, 7838-7840.
17. Cieplak, P.; Kollman, P. A. J. Mol. Recognit. 1996, 9, 103-112.
18. Gerber, P. R.; Mark, A. E.; Van Gunsteren, W. F. J. Comput.-Aided Mol. Des. 1993, 7, 305-323.
19. Liu, Z.; Berne, B. J. J. Chem. Phys. 1993, 99, 6071-6077.
20. Tidor, B. J. Phys. Chem. 1993, 97, 1069-1073.
21. Kumar, S.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A.; Rosenberg, J. M. J. Comput. Chem. 1992, 13, 1011-1021.
22. Boczko, E. M.; Brooks, C. L., III. J. Phys. Chem. 1993, 97, 4509-4513.
23. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187-217.
24. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79, 926.
25. Brunger, A.; Brooks, C. L., III; Karplus, M. Chem. Phys. Lett. 1984, 105, 495-500.
26. Ryckaert, J.-P.; Ciccotti, G.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23, 327.
27. Bennet, C. H. J. Comput. Phys. 1976, 22, 245.
28. Lee, J. Phys. Rev. Lett. 1993, 71, 211-214.
29. Hao, M.-H.; Scheraga, H. A. J. Phys. Chem. 1994, 98, 4940-4948.
30. Kumar, S.; Payne, P. W.; Vasquez, M. J. Comput. Chem. 1996, 17, 1267-1275.