An efficient hybrid explicit/implicit solvent method for biomolecular simulations

Journal of Computational Chemistry

Volumn 25, Issue 16, 2004, Pages 1967-1978

  Lee, Michael S ^a,b   Salsbury Jr , Freddie R ^c   Olson, Mark A ^b  

^a U S ARMY RESEARCH LABORATORY   (United States)

^b UNITED STATES ARMY MEDICAL RESEARCH INSTITUTE OF INFECTIOUS DISEASES   (United States)

^c WAKE FOREST UNIVERSITY   (United States)

Author keywords

Electrostatics; Generalized Born theory; Hydration; Molecular dynamics; Multigrid

Indexed keywords

COMPUTATIONAL COSTS; GENERALIZED BORN THEORY; MULTIGRID; SOLVENT METHOD; WATER MOLECULES;

CHEMICAL BONDS; ELECTROSTATICS; FREE ENERGY; HYDRATION; MACROMOLECULES; MONTE CARLO METHODS; PROTEINS; SOLVENTS;

MOLECULAR DYNAMICS;

EID: 9244224092     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/jcc.20119     Document Type: Article

References (56)

1. Allen, M. P.; Tildesley, D. J. Computer Simulation of Liquids; Oxford University Press: New York, 1987.
2. King, G.; Warshel, A. J Chem Phys 1989, 91, 3647.
3. Still, W. C.; Tempczyk, A.; Hawley, R. C.; Hendrickson, T. J Am Chem Soc 1990, 112, 6127.
4. Bursulaya, B. D.; Brooks, C. L., III. J Phys Chem B 2000, 104, 12378.
5. Calimet, N.; Schaefer, M.; Simonson, T. Proteins Struct Funct Genet 2001, 45, 144.
6. Mezei, M.; Fleming, P. J.; Srinivasan, R.; Rose, G. D. Proteins Struct Funct Biol 2004, 55, 502.
7. Sham, Y. Y.; Warshel, A. J Chem Phys 1998, 109, 7940.
8. Lee, F. S.; Warshel, A. J Chem Phys 1992, 97, 3100.
9. Masunov, A.; Lazaridis, T. J Am Chem Soc 2003, 125, 1722.
10. Beglov, D.; Roux, B. J Chem Phys 1994, 100, 9050.
11. Lounnas, V.; Ludemann, S. K.; Wade, R. C. Biophys Chem 1999, 78, 157.
12. Alper, H.; Levy, R. M. J Chem Phys 1993, 99, 9847.
13. Neumann, M.; Steinhauser, O. Mol Phys 1980, 39, 437.
14. van der Spoel, D.; van Maaren, P. J.; Berendsen, H. J. C. J Chem Phys 1998, 108, 10220.
15. Brooks, C. L., III; Karplus, M. J Chem Phys 1983, 79, 6312.
16. Brooks, C. L., III; Brünger, A.; Karplus, M. Biopolymers 1985, 24, 843.
17. Darden, T.; Pearlman, D.; Pedersen, L. G. J Chem Phys 1998, 109, 10921.
18. Essex, J. W.; Jorgensen, W. L. J Comp Chem 1995, 16, 951.
19. Kirkwood, J. G. Chem Rev 1936, 19, 275.
20. Im, W.; Berneche, S.; Roux, B. J Chem Phys 2001, 114, 2924
21. Beglov, D.; Roux, B. Biopolymers 1995, 35, 171.
22. Rosenhouse-Dantsker, A.; Osman, R. Biophys J 2000, 79, 66.
23. Kentsis, A.; Mezei, M.; Osman, R. Biophys J 2003, 84, 805.
24. Lee, M. S.; Salsbury, F. R., Jr.; Brooks, C. L., III. J Chem Phys 2002, 116, 10606
25. Lee, M. S.; Feig, M.; Salsbury, F. R., Jr.; Brooks, C. L., III. J Comp Chem 2003, 24, 1348.
26. Stote, R. H.; States, D. J.; Karplus, M. J Chim Phys 1991, 88, 2419.
27. Greengard, L.; Rokhlin, V. J Comput Phys 1987, 73, 325.
28. Sandak, B. J Comp Chem 2001, 22, 717.
29. Skeel, R. D.; Tezcan, I.; Hardy, D. J. J Comp Chem 2002, 23, 673.
30. Brooks, C. L., III; Karplus, M. J Mol Biol 1989, 208, 159.
31. Warshel, A. Chem Phys Lett 1978, 55, 454.
32. Warshel, A. J Phys Chem 1979, 83, 1640.
33. Im, W.; Beglov, D.; Roux, B. Comp Phys Commun 1998, 111, 59.
34. Im, W.; Lee, M. S.; Brooks, C. L., III. J Comp Chem 2003, 24, 1691.
35. Onufriev, A.; Case, D. A.; Bashford, D. J Comp Chem 2002, 23, 1297.
36. Salsbury, F. R., Jr.; Lee, M. S.; Feig, M.; Brooks, C. L., III, to appear.
37. Lawson, C. L. SIAM Rev 1965, 7, 415.
38. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminatham, S.; Karplus, M. J Comp Chem 1983, 4, 187.
39. Mackerell, A. D., Jr.; Bashford, D.; Bellott, M.; Dunbrack, R. L., Jr.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; Ha, S.; Joseph-McCarthy, D.; Kuchnir, L.; Kuczera, K.; Lau, F. T. K.; Mattos, C.; Michnick, S.; Ngo, T.; Nguyen, D. T.; Prodhom, B.; Reiher, W. E., III; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. J Phys Chem B 1998, 102, 3586.
40. Ryckaert, J. P.; Cicotti, G.; Berendsen, H. J. C. J Comput Phys 1977, 23, 327.
41. Lee, M. S.; Olson, M. A. J Phys Chem B, submitted.
42. O'Neill, J. W.; Kim, D. E.; Baker, D.; Zhang, K. Y. J. Acta Crystallogr D 2001, 57, 480.
43. Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. J Chem Phys 1995, 103, 8577.
44. Herce, D. H.; Darden, T.; Sagui, C. J Chem Phys 2003, 119, 7621.
45. Sheinerman, F. B.; Brooks, C. L. I. J Mol Biol 1998, 278, 439.
46. Sham, Y. Y.; Chu, Z. T.; Warshel, A. J Phys Chem B 1997, 101, 4458-4472.
47. Bogusz, S.; Cheatham, T. E. I.; Brooks, B. R. J Chem Phys 1998, 108, 7070.
48. Zhang, L. Y.; Gallichio, E.; Friesner, R. A.; Levy, R. M. J Comp Chem 2001, 22, 591.
49. Blirgi, R.; Kollman, P. A.; van Gunsteren, W. F. Proteins 2002, 47, 469.
50. Lee, F. S.; Chu, Z. T.; Warshel, A. J Comp Chem 1993, 14, 161.
51. Adams, D. J. Mol Phys 1975, 29, 307.
52. Sham, Y. Y.; Chu, Z. T.; Tao, H.; Warshel, A. Proteins Struct Funct Gene 2000, 39, 393.
53. Huo, S.; Massova, I.; Kollman, P. A. J Comp Chem 2002, 23, 15.
54. Hoogstraten, C. G.; Choe, S.; Westler, W. M.; Markley, J. L. Protein Sci 1995, 4, 2289.
55. Kurinov, I. V.; Harrison, R. W. Nat Struct Biol 1994, 1, 735.
56. Kirkwood, J. G. In Theory of Liquids; Alder, B. J., Ed.; Gordon and Breach: New York, 1968.