Evaluation of poisson solvation models using a hybrid explicit/implicit solvent method

Journal of Physical Chemistry B

Volumn 109, Issue 11, 2005, Pages 5223-5236

  Lee, Michael S ^a,b   Olson, Mark A ^a  

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

^b U S ARMY RESEARCH LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DIELECTRIC BOUNDARY; MOLECULAR SURFACES; POISSON SOLVENT MODELS; PROTEIN DYNAMICS;

COMPUTER SIMULATION; DEGREES OF FREEDOM (MECHANICS); FREE ENERGY; POISSON EQUATION; POTENTIAL ENERGY; PROTEINS; VAN DER WAALS FORCES;

SOLVENTS;

SOLVENT;

ARTICLE; CALIBRATION; CHEMICAL MODEL; CHEMISTRY; ELECTRICITY; POISSON DISTRIBUTION; PROTEIN CONFORMATION; SOLUBILITY; STATIC ELECTRICITY;

CALIBRATION; ELECTROSTATICS; MODELS, CHEMICAL; POISSON DISTRIBUTION; PROTEIN CONFORMATION; SOLUBILITY; SOLVENTS; STATIC ELECTRICITY;

EID: 15744363770     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp046377z     Document Type: Article

References (88)

1. Gilson, M. K.; Honig, B. Proteins: Struct., Funct., Genet. 1988, 4, 7.
2. Still, W. C.; Tempczyk, A.; Hawley, R. C.; Hendrickson, T. J. Am. Chem. Soc. 1990, 112, 6127.
3. Onufriev, A., Bashford, D.; Case, D. A. J. Phys. Chem. B 2000, 104, 3712.
4. Russell, S. T.; Warshel, A. J. Mol. Biol. 1985, 185, 389.
5. Hassan, S. A.; Mehler, E. L. Proteins: Struct., Funct., Genet. 2002, 47, 45.
6. Lazaridis, T.; Karplus, M. Proteins: Struct., Funct., Genet. 1999, 35, 133.
7. Wesson, L.; Eisenberg, D. Protein Sci. 1992, 1, 227.
8. Honig, B.; Nicholls, A. Science 1995, 268, 1144.
9. Cramer, C. J.; Truhlar, D. G. Chem. Rev. 1999, 99, 2161.
10. Feig, M.; Brooks, C. L., III. Proteins 2002, 49, 232.
11. Vorobjev, Y.; Hermans, J. Protein Sci. 2001, 10, 2498.
12. Lee, M. R.; Baker, D.; Kollman, P. A. J. Am. Chem. Soc. 2001, 123, 1040.
13. Bashford, D.; Gerwert, K. J. Mol. Biol. 1992, 224, 473.
14. Langen, R.; Brayer, G. D.; Berghuis, A. M.; McLendon, G.; Sherman, F.; Warshel, A. J. Mol. Biol. 1992, 224, 589.
15. Olson, M. A.; Reinke, L. T. Proteins 2000, 38, 115.
16. Huo, S.; Massova, I.; Kollman, P. A. J. Comput. Chem. 2002, 23, 15.
17. Sham, Y. Y.; Chu, Z. T.; Tao, H.; Warshel, A. Proteins: Struct., Funct., Genet. 2000, 39, 393.
18. Kollman, P. A.; Massova, I.; Reyes, C.; Kuhn, B., Huo, S.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.; Donini, O.; Cieplak, P.; Srinivasan, J.; Case, D. A.; Cheatham, T. E. I. Acc. Chem. Res. 2000, 33 889.
19. Krol, M. J. Comput. Chem. 2003, 24, 531.
20. Dominy, B. N.; Brooks, C. L. J. Phys. Chem. B 1999, 103, 3765.
21. Im, W.; Lee, M. S.; Brooks, C. L., III. J. Comput. Chem. 2003, 24, 1691.
22. Sham, Y. Y.; Chu, Z. T.; Warshel, A. J. Phys. Chem. B 1997, 101, 4458.
23. Wagoner, J.; Baker, N. A. J. Comput. Chem. 2004, 25, 1623.
24. Mezei, M.; Fleming, P. J.; Srinivasan, R.; Rose, G. D. Proteins: Struct., Funct., Genet. 2004, 55, 502.
25. Calimet, N.; Schaefer, M.; Simonson, T. Proteins: Struct., Funct., Genet. 2001, 45, 144.
26. Bursulaya, B. D.; Brooks, C. L., III. J. Phys. Chem. B 2000, 104, 12378.
27. Masunov, A.; Lazaridis, T. J. Am. Chem. Soc. 2003, 125, 1722.
28. Lee, M. S.; Salsbury, F. R., Jr.; Brooks, C. L., III. Proteins: Struct., Funct., Genet. 2004, 56, 738.
29. Feig, M.; Onufriev, A.; Lee, M. S.; Im, W.; Case, D. A.; Brooks, C. L. I. J. Comput. Chem. 2003, 25, 265.
30. Baker, N. A.; D., S.; Joseph, S.; Holst, M. J.; McCammon, J. A. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 10037.
31. Grant, J. A.; Pickup, B. T.; Nicholls, A. J. Comput. Chem. 2001, 22, 608.
32. Luo, R.; David, L.; Gilson, M. K. J. Comput. Chem. 2002, 23, 1244.
33. Sitkoff, D.; Sharp, K. A.; Honig, B. J. Phys. Chem. 1994, 98, 1978.
34. Nina, M.; Beglov, D.; Roux, B. J. Phys. Chem. B 1997, 101, 5239.
35. Lee, B.; Richards, F. M. J. Mol. Biol. 1971, 55, 151.
36. Lee, M. S.; Feig, M.; Salsbury, F. R., Jr.; Brooks, C. L., III. J. Comput. Chem. 2003, 24, 1348.
37. Schutz, C. N.; Warshel, A. Proteins: Struct., Funct., Genet. 2001, 44, 400.
38. Luo, R.; Gilson, M. K. J. Am. Chem. Soc. 2000, 122, 2934.
39. Zhang, L. Y.; Gallichio, E.; Friesner, R. A.; Levy, R. M. J. Comput. Chem. 2001, 22, 591.
40. Zhou, R.; Berne, B. J. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 12777.
41. Felts, A. K.; Harano, Y.; Gallichio, E.; Levy, R. M. Proteins: Struct., Funct., Genet. 2004, 56, 310.
42. Bogusz, S.; Cheatham, T. E. I.; Brooks, B. R. J. Chem. Phys. 1998, 108, 7070.
43. King, G.; Warshel, A. J. Chem. Phys. 1989, 91, 3647.
44. Darden, T.; Pearlman, D.; Pedersen, L. G. J. Chem. Phys. 1998, 109, 10921.
45. Lee, M. S.; Salsbury, F. R., Jr.; Olson, M. A. J. Comput. Chem. 2004, 25, 1967.
46. Beglov, D.; Roux, B. J. Chem. Phys. 1994, 100, 9050.
47. Im, W.; Berneche, S.; Roux, B. J. Chem. Phys. 2001, 114, 2924.
48. Beglov, D.; Roux, B. Biopolymers 1995, 35, 171
49. Lounnas, V.; Ludemann, S. K.; Wade, R. C. Biophys. Chem. 1999, 78, 157.
50. Im, W.; Beglov, D.; Roux, B. Comput. Phys. Commun. 1998, 111, 59.
51. Essex, J. W.; Jorgensen, W. L. J. Comput. Chem. 1995, 16, 951.
52. Herce, D. H.; Darden, T.; Sagui, C. J. Chem. Phys. 2003, 119, 7621.
53. Vorobjev, Y. N.; Hermans, J. J. Phys. Chem. B 1999, 103, 10234.
54. Hummer, G.; Pratt, L. R.; Garcia, A. E.; Garde, S. J. Phys. Chem. B 1998, 102, 3841.
55. Lee, M. S.; Salsbury, F. R., Jr.; Brooks, C. L., III. J. Chem. Phys. 2002, 116, 10606.
56. Skeel, R. D.; Tezcan, I.; Hardy, D. J. J. Comput. Chem. 2002, 23, 673.
57. Lee, F. S.; Warshel, A. J. Chem. Phys. 1992, 97, 3100.
58. Board, J. A.; Causey, J. W.; Leathrum, J. F., Windemuth, A.; Schulten, K. Chem. Phys. Lett. 1992, 198, 89.
59. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminatham, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187.
60. Mackerell, A. D., Jr.; Bashford, D.; Bellott, D. 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, I. W. E.; Roux, B.; Schlenkrich, M.; Smith, J. C.; Stole, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Yin, D.; Karplus, M. J. Phys. Chem. B 1998, 102, 3586.
61. Ryckaert, J. P.; Cicotti, G.; Berendsen, H. J. C. J. Comput. Phys. 1977, 23, 327.
62. Lawson, C. L. SIAM Rev. 1965, 7, 415.
63. Stote, R. H.; States, D. J.; Karplus, M. J. Chim. Phys. Phys.-Chim. Biol. 1991, 88, 2419.
64. Scarsi, M.; Caflisch, A. J. Comput. Chem. 1999, 20, 1533.
65. Kirkwood, J. G. In Theory of Liquids; Alder, B. J., Ed.; Gordon and Breach: New York, 1968.
66. Klapper, I.; Hagstrom, R.; Fine, R.; Sharp, K.; Honig, B. Proteins: Struct., Funct., Genet. 1986, 1, 47.
67. Kolinski, A.; Skolnick, J. Proteins: Struct., Funct., Genet. 1998, 32, 475.
68. Feig, M.; Rotkiewicz, P.; Kolinski, A.; Skolnick, J.; Brooks, C. L. I. Proteins 2000, 41, 86.
69. Sheinerman, F. B.; Brooks, C. L. I. J. Mol. Biol. 1998, 278, 439.
70. Pal, S. K.; Peon, J.; Zewail, A. H. Proc. Natl. Acad. Sci. 2002, 99, 1763.
71. Berendsen, H. J. C.; Postma, J. P. M.; van Gunsteren, W. F.; Hermans, J. Intermolecular Forces; Reidel: Dordrecht, The Netherlands, 1981.
72. Straatsma, T. P.; Berendsen, H. J. C. J. Chem. Phys. 1988, 89, 5876.
73. Nina, M.; Im, W.; Roux, B. Biophys. Chem. 1999, 78, 89.
74. Rankin, K. N.; Sulea, T.; Purisima, E. O. J. Comput. Chem. 2003, 24, 954.
75. Allen, M. P.; Tildesley, D. J. Computer Simulation of Liquids; Oxford University Press: New York, 1987.
76. Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. J. Chem. Phys. 1995, 103, 8577.
77. van der Spoel, D.; van Maaren, P. J.; Berendsen, H. J. C. J. Chem. Phys. 1998, 108, 10220.
78. Edelsbrunner, H.; Facello, M.; Fu, P.; Liang, J. Measuring Proteins and Voids in Proteins. Proceedings of the 28th Annual Hawaii International Conference System Sciences; IEEE Computer Society Press: Los Alamitos, CA, 1995; Vol. 5, p 256.
79. Ibragimova, G. T.; Wade, R. C. Biophys. J. 1998, 75, 2906.
80. Marcus, Y. J. Chem. Soc., Faraday Trans. 1991, 87, 2995.
81. Ashbaugh, H. S. J. Phys. Chem. B 2000, 104, 7235.
82. Babu, C. S.; Lim, C. J. Chem. Phys. 2001, 114, 889.
83. Simmerling, C.; Lee, M. R.; Ortiz, A. R.; Kolinski, A.; Skolnick, J.; Kollman, P. A. J. Am. Chem. Soc. 2000, 122, 8392.
84. Bucher, M.; Porter, T. L. J. Phys. Chem. 1986, 90, 3406.
85. Feig, M.; Lee, M. S. Work in progress.
86. Rapp, C. S.; Friesner, R. A. Proteins: Struct., Funct., Genet. 1999, 35, 173.
87. Huo, S.; Massova, I.; Kollman, P. A. J. Comput. Phys. 2002, 23, 15.
88. Halkier, A.; Koch, H.; Jorgensen, P.; Christiansen, O.; Nielsen, I. M. B.; Helgaker, T. Theor. Chem. Acc. 1997, 97, 150.