The SGB/NP hydration free energy model based on the surface generalized born solvent reaction field and novel nonpolar hydration free energy estimators

Journal of Computational Chemistry

Volumn 23, Issue 5, 2002, Pages 517-529

  Gallicchio, Emilio ^a   Zhang, Linda Yu ^a   Levy, Ronald M ^a  

^a RUTGERS UNIVERSITY   (United States)

Author keywords

Generalized Born model; Hydration free energy prediction; Hydrophobic hydration; Solvation; Solvent potential of mean force

Indexed keywords

HYDROCARBON; SOLVENT; WATER;

ALGORITHM; ARTICLE; CHEMICAL MODEL; CHEMISTRY; COMPUTER SIMULATION; ENERGY TRANSFER; HYDROGEN BOND; THERMODYNAMICS;

ALGORITHMS; COMPUTER SIMULATION; ENERGY TRANSFER; HYDROCARBONS; HYDROGEN BONDING; MODELS, CHEMICAL; SOLVENTS; THERMODYNAMICS; WATER;

EID: 0037089017     PISSN: 01928651     EISSN: None     Source Type: Journal    
DOI: 10.1002/jcc.10045     Document Type: Article

References (35)

1. 1 Lazaridis, T. ; Archontis, G. ; Karplus, M. Adv Protein Chem 1995, 47, 262.
2. 2 Honig, B. ; Yang, A. Adv Protein Chem 1995, 46, 27.
3. 3 Dill, K. A. Biochemistry 1990, 29, 7133.
4. 4 Gilson, M. K. ; Given, J. A. ; Bush, B. L. ; McCammon, J. A. Biophysical J 1997, 72, 1047.
5. 5 Apostolakis, J. ; Ferrara, P. ; Calfish, A. J Chem Phys 1999, 110, 2099.
6. 6 Levy, R. M. ; Gallicchio, E. Annu Rev Phys Chem 1998, 49, 531.
7. 7 Roux, B. ; Simonson, T. Biophy Chem 1999, 78, 1.
8. 8 Lazaridis, T. ; Karplus, M. Curr Opin Struct Biol 2000, 10, 139.
9. 9 Wallqvist, A. ; Gallicchio, E. ; Felts, A. K. ; Levy, R. M. Adv Chem Phys 2001, to appear.
10. 10 Ghosh, A. ; Rapp, C. S. ; Friesner, R. A. J Phys Chem B 1998, 102, 10983.
11. 11 Zauhar, R. J. ; Morgan, R. S. J Mol Biol 1985, 186, 815.
12. 12 Honig, B. ; Sharp, K. ; Yang, A. J Phys Chem 1993, 97, 1101.
13. 13 Zhang, L. ; Gallicchio, E. ; Friesner, R. ; Levy, R. M. J Comp Chem 2001, 22, 591.
14. 14 Gallicchio, E. ; Kubo, M. M. ; Levy, R. M. J Phys Chem B 2000, 104, 6271.
15. 15 Pitera, J. W. ; van Gunsteren, W. F. J Am Chem Soc 2001, 123, 3163.
16. 16 Still, W. C. ; Tempczyk, A. ; Hawley, R. C. ; Hendrikson, T. J Am Chem Soc 1990, 112, 6127.
17. 17 Nina, M. ; Beglov, D. ; Roux, B. J Phys Chem B 1997, 101, 5239.
18. 18 Dominy, B. N. ; Brooks, C. L. I. J Phys Chem B 1999, 103, 3765.
19. 19 Onufriev, A. ; Bashford, D. ; Case, D. A. J Phys Chem B 2000, 104, 3712.
20. 20 Jorgensen, W. L. ; Maxwell, D. S. ; Tirado–Rives, J. J Am Chem Soc 1996, 118, 11225.
21. 21 Zhang, L. ; Gallicchio, E. ; Levy, R. M. In AIP Conference Proceedings (Simulation and Theory of Electrostatic Interactions in Solutions), Vol. 492; 1999.
22. 22 Ashbaugh, H. S. ; Kaler, E. W. ; Paulaitis, M. E. J Am Chem Soc 1999, 121, 9243.
23. 23 Cabani, S. ; Gianni, P. ; Mollica, V. ; Lepori, L. J Solut Chem 1981, 10, 563.
24. 24 Qiu, D. ; Shenkin, P. S. ; Hollinger, F. P. ; Still, C. W. J Phys Chem A 1997, 101, 3005.
25. 25 Sitkoff, D. ; Sharp, K. A. ; Honig, B. J Phys Chem 1994, 98, 1978.
26. 26 Eisenberg, D. ; McLachlan, A. D. Nature 1986, 319, 199.
27. 27 Ooi, T. ; Oobatake, M. ; Nemethy, G. ; Sheraga, A. Proc Natl Acad Sci USA 1987, 84, 3086.
28. 28 Privalov, P. L. ; Makhatadze, G. I. J Mol Biol 1993, 232, 660.
29. 29 Kitchen, D. B. ; Hirata, F. ; Westbrook, J. D. ; Levy, R. M. ; Kofke, D. ; Yarmush, M. J Comput Chem 1990, 11, 1169.
30. 30 Ding, Y. ; Bernardo, D. N. ; Krogh–Jespersen, K. ; Levy, R. M. J Phys Chem 1995, 99, 11575.
31. 31 Kubo, M. F. ; Gallicchio, E. ; Levy, R. M. J Phys Chem 1997, 101, 10527.
32. 32 Marten, B. ; Kim, K. ; Cortis, C. ; Friesner, R. A. ; Murphy, R. B. ; Ringnalda, M. N. ; Sitkoff, D. ; Honig, B. J Phys Chem 1996, 100, 11775.
33. 33 Rizzo, R. C. ; Jorgensen, W. L. J Am Chem Soc 1999, 121, 4827.
34. 34 Sitkoff, D. ; Sharp, K. A. ; Honig, B. Biophys Chem 1994, 51, 397.
35. 35 Hawkins, G. D. ; Cramer, C. J. ; Truhlar, D. G. J Phys Chem 1996, 100, 19824. CW000104‐TI