Efficient computation of the total solvation energy of small molecules via the r6 generalized born model

Journal of Chemical Theory and Computation

Volumn 8, Issue 7, 2012, Pages 2404-2411

  Aguilar, Boris ^a   Onufriev, Alexey V ^a  

^a State University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84863694107     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct200786m     Document Type: Article

References (37)

1. Jorgensen, W. L. Science 2004, 303, 1813-1818
2. Mobley, D. L.; Dill, K. A. Structure 2009, 17, 489-498
3. Shirts, M. R.; L., M. D.; Brown, S. P. In Structure Based Drug Design, 1st ed.; Merz, K. M.; Ringe, D.; Reynolds, C. H., Eds.; Lecture Notes in Computer Science; Cambridge University Press: New York, 2010; pp 61-85
4. Gilson, M. K.; Zhou, H. X. Annu. Rev. Biophys. Biomol. Struct. 2007, 36, 21-42
5. Llinàs, A.; Glen, R. C.; Goodman, J. M. J. Chem. Inf. Model. 2008, 48, 1289-1303
6. Nicholls, A.; Mobley, D. L.; Guthrie, J. P.; Chodera, J. D.; Bayly, C. I.; Cooper, M. D.; Pande, V. S. J. Med. Chem. 2008, 51, 769-779
7. Shivakumar, D.; Deng, Y.; Roux, B. J. Chem. Theory Comput. 2009, 5, 919-930
8. Mobley, D. L.; Bayly, C. I.; Cooper, M. D.; Shirts, M. R.; Dill, K. A. J. Chem. Theory Comput. 2009, 5, 350-358
9. Nicholls, A.; Wlodek, S.; Grant, J. J. Comput.-Aided Mol. Des. 2010, 24, 293-306
10. Nicholls, A.; Wlodek, S.; Grant, J. A. J. Phys. Chem. B 2009, 113, 4521-4532
11. Labute, P. J. Comput. Chem. 2008, 29, 1693-1698
12. Mobley, D. L.; Dill, K. A.; Chodera, J. D. J. Phys. Chem. B 2008, 112, 938-946
13. Feig, M.; Onufriev, A.; Lee, M. S.; Im, W.; Case, D. A.; Brooks, C. L. J. Comput. Chem. 2004, 25, 265-284
14. Onufriev, A. In Modeling Solvent Environments, 1st ed.; Feig, M., Ed.; Wiley-VCH Verlag GmbH & Co. KGaA: Weinheim, Germany, 2010; pp 127-165
15. Bashford, D.; Case, D. A. Annu. Rev. Phys. Chem. 2000, 51, 129-152
16. Feig, M.; Brooks, C. L. Curr. Opin. Struct. Biol. 2004, 14, 217-224
17. Knight, J. L.; Brooks, C. L. J. Comput. Chem. 2011, 32, 2909-2923
18. Aguilar, B.; Shadrach, R.; Onufriev, A. V. J. Chem. Theory Comput. 2010, 6, 3613-3630
19. Tjong, H.; Zhou, H. X. J. Phys. Chem. B 2007, 111, 3055-3061
20. Lee, B.; Richards, F. M. J. Mol. Biol. 1971, 55, 379
21. Mongan, J.; Svrcek-Seiler, A.; Onufriev, A. J. Chem. Phys. 2007, 127, 185101-185101
22. Sigalov, G.; Fenley, A.; Onufriev, A. J. Chem. Phys. 2006, 124, 124902
23. Still, W. C.; Tempczyk, A.; Hawley, R. C.; Hendrickson, T. J. Am. Chem. Soc. 1990, 112, 6127-6129
24. Svrcek-Seiler, A. personal communication, 2001
25. Grycuk, T. J. Chem. Phys. 2003, 119, 4817-4826
26. Sanner, M. F.; Olson, A. J.; Spehner, J. C. Biopolymers 1996, 38, 305-320
27. Bondi, A. J. Phys. Chem. 1964, 68, 441-451
28. Sitkoff, D.; Sharp, K. A.; Honig, B. J. Phys. Chem. 1994, 98, 1978-1988
29. Tan, C.; Tan, Y.-H.; Luo, R. J. Phys. Chem. B 2007, 111, 12263-12274
30. Wagoner, J. A.; Baker, N. A. Proc. Natl. Acad. Sci. U.S.A. 2006, 103, 8331-8336
31. Zacharias, M. J. Phys. Chem. A 2003, 107, 3000-3004
32. Gallicchio, E.; Levy, R. M. J. Comput. Chem. 2004, 25, 479-499
33. Nelder, J. A.; Mead, R. Comput. J. 1965, 7, 308-315
34. Grant, J. A.; Pickup, B. T.; Nicholls, A. J. Comput. Chem. 2001, 22, 608-640
35. Fennell, C. J.; Kehoe, C. W.; Dill, K. A. Proc. Natl. Acad. Sci. U.S.A. 2011, 108, 3234-3239
36. Hawkins, G. D.; Cramer, C. J.; Truhlar, D. G. J. Phys. Chem. 1996, 100, 19824-19839
37. Case, D. A. AMBER 9; University of California: San Francisco, CA, 2006