Continuum solvation models in the linear interaction energy method

Journal of Physical Chemistry B

Volumn 110, Issue 24, 2006, Pages 12034-12041

  Carlsson, Jens ^a   Andér, Martin ^a   Nervall, Martin ^a   Åqvist, Johan ^a  

^a UPPSALA UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; COMPLEXATION; COMPUTER SIMULATION; ELECTRIC POWER MEASUREMENT; FREE ENERGY; LINEAR SYSTEMS; MATHEMATICAL MODELS; PARAMETER ESTIMATION; POISSON DISTRIBUTION; PROTEINS; SOLVENT EXTRACTION;

CONTINUUM SOLVATION MODELS; GENERALIZED BORN (GB) CONTINUUM MODELS; LINEAR INTERACTION ENERGY (LIE) METHOD; PROTEIN-LIGAND COMPLEXES;

CONTINUUM MECHANICS;

EID: 33745799052     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp056929t     Document Type: Article

References (42)

1. Brandsdal, B. O.; Österberg, F.; Almlöf, M.; Feierberg, I.; Luzhkov, V. B.; Åqvist, J. Adv. Protein Chem. 2003, 66, 123.
2. Gohlke, H.; Klebe, G. Angew. Chem., Int. Ed. 2002, 41, 2645.
3. Åqvist, J.; Medina, C.; Samuelsson, J. E. Protein Eng. 1994, 7, 385.
4. Åqvist, J.; Hansson, T. J. Phys. Chem. 1996, 100, 9512.
5. Hansson, T.; Marelius, J.; Åqvist, J. J. Comput.-Aided Mol. Des. 1998, 12, 27.
6. Carlson, H. A.; Jorgensen, W. L. J. Phys. Chem. 1995, 99, 10667.
7. Almlöf, M.; Brandsdal, B. O.; Åqvist, J. J. Comput. Chem. 2004, 25, 1242.
8. Baker, N. A. Curr. Opin. Struct. Biol. 2005, 15, 137.
9. Feig, M.; Brooks, C. L. Curr. Opin. Struct. Biol. 2004, 14, 217.
10. Gouda, H.; Kuntz, I. D.; Case, D. A.; Kollman, P. A. Biopolymers 2003, 68, 16.
11. Zhang, L. Y.; Gallicchio, E.; Friesner, R. A.; Levy, R. M. J. Comput. Chem. 2001, 22, 591.
12. Warwicker, J.; Watson, H. C. J. Mol. Biol. 1982, 157, 671.
13. Still, W. C.; Tempczyk, A.; Hawley, R. C.; Hendrickson, T. J. Am. Chem. Soc. 1990, 112, 6127.
14. Zhu, J.; Alexov, E.; Honig, B. J. Phys. Chem. B 2005, 109, 3008.
15. Qiu, D.; Shenkin, P. S.; Hollinger, F. P.; Still, W. C. J. Phys. Chem. A 1997, 101, 3005.
16. Jayaram, B.; Liu, Y.; Beveridge, D. L. J. Chem. Phys. 1998, 109, 1465.
17. Onufriev, A.; Case, D. A.; Bashford, D. J. Comput. Chem. 2002, 23, 1297.
18. Srinivasan, J.; Cheatham, T. E.; Cieplak, P.; Kollman, P. A.; Case, D. A. J. Am. Chem. Soc. 1998, 120, 9401.
19. Kollman, P. A.; Massova, I.; Reyes, C.; Kuhn, B.; Huo, S. H.; Chong, L.; Lee, M.; Lee, T.; Duan, Y.; Wang, W.; Donini, O.; Cieplak, P.; Srinivasan, J.; Case, D. A.; Cheatham, T. E. Acc. Chem. Res. 2000, 33, 889.
20. Kuhn, B.; Kollman, P. A. J. Med. Chem. 2000, 43, 3786.
21. Marelius, J.; Hansson, T.; Åqvist, J. Int. J. Quantum Chem. 1998, 69, 77.
22. Chang, C. E.; Chen, W.; Gilson, M. K. J. Chem. Theory Comput. 2005, 1, 1017.
23. Huo, S. H.; Wang, J. M.; Cieplak, P.; Kollman, P. A.; Kuntz, I. D. J. Med. Chem. 2002, 45, 1412.
24. Zhou, R. H.; Friesner, R. A.; Ghosh, A.; Rizzo, R. C.; Jorgensen, W. L.; Levy, R. M. J. Phys. Chem. B 2001, 105, 10388.
25. Ghosh, A.; Rapp, C. S.; Friesner, R. A. J. Phys. Chem. B 1998, 102, 10983.
26. Krol, M. J. Comput. Chem. 2003, 24, 531.
27. David, L.; Luo, R.; Gilson, M. K. J. Comput. Chem. 2000, 21, 295.
28. Zhou, R. H.; Berne, B. J. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 12777.
29. Ersmark, K.; Nervall, M.; Hamelink, E.; Janka, L. K.; Clemente, J. C.; Dunn, B. M.; Blackman, M. J.; Samuelsson, B.; Åqvist, J.; Hallberg, A. J. Med. Chem. 2005, 48, 6090.
30. Marelius, J.; Kolmodin, K.; Feierberg, I.; Åqvist, J. J. Mol. Graphics Modell. 1998, 16, 213.
31. van Gunsteren, W. F.; Berendsen, H. J. C. Groningen Molecular Simulation (GROMOS) Library Manual; Biomos B. V.: Nijenborgh, Groningen, The Netherlands, 1987.
32. Rocchia, W.; Sridharan, S.; Nicholls, A.; Alexov, E.; Chiabrera, A.; Honig, B. J. Comput. Chem. 2002, 23, 128.
33. Rocchia, W.; Alexov, E.; Honig, B. J. Phys. Chem. B 2001, 105, 6507.
34. Sitkoff, D.; Sharp, K. A.; Honig, B. J. Phys. Chem. 1994, 98, 1978.
35. Zoete, V.; Michielin, O.; Karplus, M. J. Comput. Aided Mol. Des. 2003, 17, 861.
36. Huang, D.; Caflisch, A. J. Med. Chem. 2004, 47, 5791.
37. Marelius, J.; Ljungberg, K. B.; Åqvist, J. Eur. J. Pharm. Sci. 2001, 14, 87.
38. Feig, M.; Onufriev, A.; Lee, M. S.; Im, W.; Case, D. A.; Brooks, C. L. J. Comput. Chem. 2004, 25, 265.
39. Jorgensen, W. L.; Tiradorives, J. J. Am. Chem. Soc. 1988, 110, 1657.
40. Nina, M.; Beglov, D.; Roux, B. J. Phys. Chem. B 1997, 101, 5239.
41. Swanson, J. M. J.; Adcock, S. A.; McCammon, J. A. J. Chem. Theory Comput. 2005, 1, 484.
42. Sham, Y. Y.; Chu, Z. T.; Tao, H.; Warshel, A. Proteins 2000, 39, 393.