Coupling the level-set method with molecular mechanics for variational implicit solvation of nonpolar molecules

Journal of Chemical Theory and Computation

Volumn 5, Issue 2, 2009, Pages 257-266

  Cheng, Li Tien ^a   Xie, Yang ^b   Dzubiella, Joachim ^c   Andrew McCammon, J ^a   Jianwei Che, ^d   Li, Bo ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF CALIFORNIA   (United States)

^c TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^d GENOMICS INSTITUTE OF THE NOVARTIS RESEARCH FOUNDATION   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 65249120770     PISSN: 15499618     EISSN: None     Source Type: Journal    
DOI: 10.1021/ct800297d     Document Type: Article

References (32)

1. Roux, B.; Simonson, T. Biophys. Chem. 1999, 78, 1-20.
2. Feig, M.; Brooks III, C. L. Curr. Opin. Struct. Biol. 2004, 14, 217-224.
3. Connolly, M. L. J. Appl. Crystallogr. 1983, 16, 548-558.
4. Connolly, M. L. J. Mol. Graphics 1992, 11, 139-141.
5. Lee, B.; Richards, F. M. J. Mol. Biol. 1971, 55, 379-400.
6. Richards, F. M. Annu. Rev. Biophys. Bioeng. 1977, 6, 151-176.
7. Richmond, T. J. J. Mol. Biol. 1984, 178, 63-89.
8. Fixman, F. J. Chem. Phys. 1979, 70, 4995-5005.
9. Davis, M. E.; McCammon, J. A. Chem. Rev. 1990, 90, 509-521.
10. Sharp, K. A.; Honig, B. J. Phys. Chem. 1990, 94, 7684-7692.
11. Still, W. C.; Tempczyk, A.; Hawley, R. C.; Hendrickson, T. J. Am. Chem. Soc. 1990, 112, 6127-6129.
12. Bashford, D.; Case, D. A. Annu. Rev. Phys. Chem. 2000, 51, 129-152.
13. Baker, N. A. Curr. Opin. Struct. Biol. 2005, 15, 137-143.
14. Lum, K.; Chandler, D.; Weeks, J. D. J. Phys. Chem. B 1999, 103, 4570-4577.
15. Chandler, D. Nature 2005, 437, 640-647.
16. Chen, J.; Brooks III, C. L. J. Am. Chem. Soc. 2007, 129, 2444.
17. Dzubiella, J.; Swanson, J. M. J.; McCammon, J. A. Phys. Rev. Lett. 2006, 96, 087802.
18. Dzubiella, J.; Swanson, J. M. J.; McCammon, J. A. J. Chem. Phys. 2006, 124, 084905.
19. Cheng, L.-T.; Dzubiella, J.; McCammon, J. A.; Li, B. J. Chem. Phys. 2007, 127, 084503.
20. Can, T.; Chen, C.-I.; Wang, Y.-F. J. Mol. Graphics Modell. 2006, 25, 442-454.
21. Tolman, R. C. J. Chem. Phys. 1949, 17, 333-337.
22. Buff, F. P. J. Chem. Phys. 1951, 19, 1591-1594.
23. Stillinger, F. H. J. Soln. Chem. 1973, 2, 141-158.
24. Ashbaugh, H. S.; Pratt, L. R. Rev. Mod. Phys. 2006, 78, 159-178.
25. Che, J.; Dzubiella, J.; Li, B.; McCammon, J. A. J. Phys. Chem. B 2008, 112, 3058-3069.
26. Osher, S.; Fedkiw, R. Level Set Methods and Dynamic Implicit Surfaces; Springer: New York, 2002.
27. Osher, S.; Sethian, J. A. J. Comput. Phys. 1988, 79, 12-49.
28. Sethian, J. A. Level Set Methods and Fast Marching Methods: Evolving Interfaces in Geometry, Fluid Mechanics, Computer Vision, and Materials Science, 2nd ed.; Cambridge University Press: 1999.
29. Halgren, T. A. J. Comput. Chem. 1996, 17, 490-519.
30. Halgren, T. A. J. Comput. Chem. 1996, 17, 553-586.
31. Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. J. Am. Chem. Soc. 1996, 118, 11225-11236.
32. Machida, K. Principles of Molecular Mechanics; Kodansha and Wiley: 1999.