Generalized Born Model with a Simple Smoothing Function

Journal of Computational Chemistry

Volumn 24, Issue 14, 2003, Pages 1691-1702

  Im, Wonpil ^a   Lee, Michael S ^a   Brooks III, Charles L ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

Born model; Poisson Boltzmann; Smoothing function

Indexed keywords

DIELECTRIC MATERIALS; ELECTROSTATICS; FINITE DIFFERENCE METHOD; VACUUM APPLICATIONS;

GENERALIZED BORN MODEL;

PROTEINS;

PROTEIN; SOLVENT;

ARTICLE; CHEMISTRY; COMPARATIVE STUDY; ELECTRICITY; ENERGY TRANSFER; HYDROGEN BOND; MACROMOLECULE; MATHEMATICAL COMPUTING; PROTEIN CONFORMATION; THEORETICAL MODEL; THERMODYNAMICS;

ELECTROSTATICS; ENERGY TRANSFER; HYDROGEN BONDING; MACROMOLECULAR SUBSTANCES; MATHEMATICAL COMPUTING; MODELS, THEORETICAL; PROTEIN CONFORMATION; PROTEINS; SOLVENTS; THERMODYNAMICS;

EID: 0141956090     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/jcc.10321     Document Type: Article

References (43)

1. Brooks, C. L., III; Karplus, M.; Pettitt, B. M. In Advances in Chemical Physics; Prigogine, I., Rice, S. A., Eds.; John Wiley & Sons: New York, 1988, vol. LXXI.
2. Roux, B.; Simonson, T. Biophys Chem 1999, 78, 1.
3. Warwicker, J.; Watson, H. C. J Mol Biol 1982, 157, 671.
4. Klapper, I.; Hagstrom, R.; Fine, R.; Sharp, K.; Honig, B. Proteins 1986, 1, 47.
5. Nicholls, A.; Honig, B. J Comput Chem 1991, 12, 435.
6. Honig, B.; Nicholls, A. Science 1995, 268, 1144.
7. Roux, B.; Bernèche, S.; Im, W. Biochemistry 2000, 39, 13295.
8. Murray, D.; Honig, B. Mol Cell 2002, 9, 145.
9. David, L.; Luo, R.; Gilson, M. J Comput Chem 2000, 21, 295.
10. Luo, R.; David, L.; Gilson, M. J Comput Chem 2002, 23, 1244.
11. Born, M. Z Phys 1920, 1, 45.
12. Still, W. C.; Tempczyk, A.; Hawley, R. C.; Hendrickson, T. J Am Chem Soc 1990, 112, 6127.
13. Hawkins, G. D.; Cramer, C. J.; Truhlar, D. G. J Phys Chem 1996, 100, 19824.
14. Schaefer, M.; Karplus, M. J Phys Chem 1996, 100, 1578.
15. iu, D.; Shenkin, P. S.; Hollinger, F. P.; Still, W. C. J Phys Chem A 1997, 101, 3005.
16. Scarsi, M.; Apostolakis, J.; Caflisch, A. J Phys Chem A 1997, 101, 8098.
17. Ghosh, A.; Rapp, C. S.; Friesner, R. A. J Phys Chem B 1998, 102, 10983.
18. Dominy, B. N.; Brooks, C. L., III. J Phys Chem B 1999, 103, 3765.
19. Srinivasan, J.; Trevathan, M. W.; Beroza, P.; Case, D. A. Theor Chem Acc 1999, 101, 426.
20. Onufriev, A.; Bashford, D.; Case, D. A. J Phys Chem B 2000, 104, 3712.
21. Lee, M. S.; Salsbury, F. R., Jr.; Brooks, C. L., III. J Chem Phys 2002, 116, 10606.
22. Spassov, V. Z.; Yan, L.; Szalma, S. J Phys Chem B 2002, 106, 8726.
23. Onufriev, A.; Bashford, D.; Case, D. A. J Comput Chem 2002, 23, 1297.
24. Lee, M. S.; Feig, M.; Salsbury, F. R., Jr.; Brooks, C. L., III. J Comput Chem, 2003, 24, 1348.
25. Lee, B.; Richards, F. M. J Mol Biol 1971, 55, 379.
26. Richards, F. M. Annu Rev Biophys Bioeng 1977, 6, 151.
27. Gilson, M. K.; Davis, M. E.; Luty, B. A.; McCammon, J. A. J Phys Chem 1993, 97, 3591.
28. Im, W.; Beglov, D.; Roux, B. Comput Phys Commun 1998, 111, 59.
29. Hermann, R. B. J Phys Chem 1972, 76, 2754.
30. Simonson, T.; Brunger, A. J Phys Chem 1994, 98, 4683.
31. Sharp, K. A.; Honig, B. Annu Rev Biophys Biophys Chem 1990, 19, 301.
32. Nina, M.; Im, W.; Roux, B. Biophys Chem 1999, 78, 89.
33. Nina, M.; Beglov, D.; Roux, B. J Phys Chem B 1997, 101, 5239.
34. Press, W. H.; Flannery, B. P.; Teukolsky, S. A.; Vetterling, W. T. Numerical Recipes: The Art of Scientific Computing; Cambridge University Press: Cambridge, MA, 1989.
35. Lebedev, V. I.; Laikov, D. N. Doklady Math 1999, 59, 477.
36. Roux, B. Biophys J 1997, 73, 2980.
37. Im, W.; Bernèche, S.; Roux, B. J Chem Phys 2001, 114, 2924.
38. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J Comput Chem 1983, 4, 187.
39. MacKerell, A. D., Jr.; Bashford, D.; Bellot, M.; Dunbrack, R. L.; Evanseck, J. D.; Field, M. J.; Fischer, S.; Gao, J.; Guo, H.; S. Ha, D. J.-M.; 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.; Stote, R.; Straub, J.; Watanabe, M.; Wiorkiewicz-Kuczera, J.; Karplus, M. J Phys Chem B 1998, 102, 3586.
40. Berman, H. M.; Westbrook, J.; Feng, Z.; Gilliland, G.; Bhat, T. N.; Weissig, H.; Shindyalov, I. N.; Bourne, P. E. Nucleic Acids Res 2000, 28, 235.
41. Wikstrom, M.; Drakenberg, T.; Forsen, S.; Sjobring, U.; Bjorck, L. Biochemistry 1994, 33, 14011.
42. Banavali, N. K.; Im, W.; Roux, B. J Chem Phys 2002, 117, 7381.
43. Banavali, N. K.; Roux, B. J Phys Chem B 2002, 106, 11026.