Sensitivity analysis and charge-optimization for flexible ligands: Applicability to lead optimization

Journal of Chemical Theory and Computation

Volumn 2, Issue 2, 2006, Pages 259-270

  Gilson, Michael K ^a  

^a UNIVERSITY OF MARYLAND BIOTECHNOLOGY INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 33846254079     PISSN: 15499618     EISSN: None     Source Type: Journal    
DOI: 10.1021/ct050226y     Document Type: Article

References (40)

1. Gilson, M. K.; Honig, B. Proc. Natl. Acad. Sci. U.S.A. 1989, 86, 1524-1528.
2. Hendsch, Z. S.; Tidor, B. Protein Sci. 1994, 3, 211-226.
3. Lee, L. P.; Tidor, B. J. Chem. Phys. 1997, 106, 8681-8690.
4. Kangas, E.; Tidor, B. J. Chem. Phy. 1998, 109, 7522-7545.
5. Sulea, T.; Purisima, E. O. J. Phys. Chem. B 2001, 105, 889-899.
6. Kangas, E.; Tidor, B. J. Phys. Chem. B 2001, 105, 880-888.
7. Sulea, T.; Purisima, E. O. Biophys. J. 2003, 84, 2883-2896.
8. Mandal, A.; Hilvert, D. J. Am. Chem. Soc. 2003, 125, 5598-5599.
9. Sims, P. A.; Wong, C. F.; McCammon, J. A. J. Comput. Chem. 2004, 25, 1416-1429.
10. Bardhan, J. P.; Lee, J. H.; Kuo, S. S.; Tidor, M. D. A. B.; White, J. K. Fast methods for biomolecule charge optimization. In Technical proceedings of the 2003 Nanotechnology Conference and Trade Show; Nanoscience and Technology Institute: Cambridge, MA, 2003.
11. Bardhan, J. P.; Lee, J. H.; Altman, M. D.; Leyffer, S.; Benson, S.; Tidor, B.; White, J. K. Biomolecule electrostatic optimization with an implicit Hessian. In Technical proceedings of the 2004 Nanotechnology Conference and Trade Show; Nanoscience and Technology Institute: Cambridge, MA, 2004.
12. Zhang, H.; Wong, C. F.; Thacher, T.; Rabitz, H. Proteins: Struct., Funct., Genet. 1995, 23, 218-232.
13. Wong, C. F.; Thacher, T.; Rabitz, H. Sensitivity analysis in biomolecular simulation. In Rev. Comput. Chem.; Wiley-VCH: New York, 1998.
14. Sims, P. A.; Wong, C. F.; McCammon, J. A. J. Med. Chem. 2003, 46, 3314-3325.
15. Gilson, M. K.; Given, J. A.; Bush, B. L.; McCammon, J. A. Biophys. J. 1997, 72, 1047-1069.
16. Hill, T. L. Statistical Mechanics. Principles and selected applications; McGraw-Hill: New York, 1956.
17. Cieplak, P.; Pearlman, D. A.; Kollman, P. A. J. Chem. Phys. 1994, 101, 627-633.
18. Gilson, M. K.; Rashin, A. A.; Fine, R.; Honig, B. J. Mol. Biol. 1985, 183, 503-516.
19. Arfken, G. Mathematical Methods for Physicists, 3rd ed.; Academic Press: Orlando, FL, 1985.
20. Lam, P. Y. S.; Jadhav, P. K.; Eyermann, C. J.; Hodge, C. N.; Ru, Y.; Bacheler, L. T.; Meek, J. L.; Otto, M. J.; Rayner, M. M.; Wong, Y. N.; Chang, C.; Weber, P. C.; Jackson, D. A.; Sharpe, T. R.; Erickson-Viitanen, S. Science 1994, 263, 380-384.
21. Lam, P. Y.; Jadhav, P. K.; Eyermann, C. J.; Hodge, C. N.; Ru, Y.; Bacheler, L. T.; Meek, J. L.; Otto, M. J.; Rayner, M. M.; et al., Y. N. W. Science 1994, 265, 380-384.
22. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187-217.
23. Accelrys, Inc. San Diego, CA,.
24. David, L.; Luo, R.; Gilson, M. K. J. Comput.-Aided Mol. Des. 2001, 15, 157-171.
25. Kairys, V.; Gilson, M. K. J. Comput. Chem. 2002, 23, 1656-1670.
26. van Gunsteren, W. F.; Berendsen, H. J. C. Mol. Simul. 1988, 1, 173-185.
27. Davis, M. E.; Madura, J. D.; Luty, B. A.; McCammon, J. A. Comput. Phys. Commun. 1991, 62, 187-197.
28. Richards, F. M. Annu. Rev. Biophys. Bioeng. 1977, 6, 151-176.
29. Warwicker, J.; Watson, H. C. J. Mol. Biol. 1982, 157, 671-679.
30. Klapper, I.; Hagstrom, R.; Fine, R.; Sharp, K.; Honig, B. Proteins: Struct., Funct., Genet. 1986, 1, 47-79.
31. Gilson, M. K.; Sharp, K. A.; Honig, B. H. J. Comput. Chem. 1988, 9, 327-335.
32. Anderson, E.; Bai, Z.; Bischof, C.; Blackford, S.; Demmel, J.; Dongarra, J.; Du Croz, J.; Greenbaum, A.; Hammarling, S.; McKenney, A.; Sorensen, D. LAPACK Users' Guide; Society for Industrial and Applied Mathematics: Philadelphia, PA, 3rd ed.; 1999.
33. http://www.netlib.org/opt/praxis.
34. http://www.netlib.org.
35. Qiu, D.; Shenkin, P. S.; Hollinger, F. P.; Still, W. C. J. Phys. Chem. 1997, 101, 3005-3014.
36. Ghosh, A.; Rapp, C. S.; Friesner, R. A. J. Phys. Chem. B 1998, 102, 10983-10990.
37. Jayaram, B.; Liu, Y.; Beveridge, D. L. J. Chem. Phys. 1998, 109, 1465-1471.
38. Dominy, B. N.; Brooks, C. L., III. J. Phys. Chem. B 1999, 103, 3765-3773.
39. Lee, M. S.; Salsbury, F. R., Jr.; Charles L.; Brooks, I.
40. Im, W.; Lee, M. S.; Brooks, C. L., III. J. Comput. Chem. 2003, 24, 1691-1702.