On the role of dewetting transitions in host-guest binding free energy calculations

Journal of Chemical Theory and Computation

Volumn 9, Issue 1, 2013, Pages 46-53

  Rogers, Kathleen E ^a   Ortiz Sánchez, Juan Manuel ^a   Baron, Riccardo ^a,b   Fajer, Mikolai ^a   De Oliveira, César Augusto F ^a   McCammon, J Andrew ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b UNIVERSITY OF UTAH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84872145772     PISSN: 15499618     EISSN: 15499626     Source Type: Journal    
DOI: 10.1021/ct300515n     Document Type: Article

References (42)

1. Freeman, W. A.; Mock, W. L.; Shih, N. Y. J. Am. Chem. Soc. 1981, 103 (24) 7367-7368
2. Kim, J.; Jung, I. S.; Kim, S. Y.; Lee, E.; Kang, J. K.; Sakamoto, S.; Yamaguchi, K.; Kim, K. J. Am. Chem. Soc. 2000, 122 (3) 540-541
3. Liu, S.; Ruspic, C.; Mukhopadhyay, P.; Chakrabarti, S.; Zavalij, P. Y.; Isaacs, L. J. Am. Chem. Soc. 2005, 127 (45) 15959-15967
4. Rekharsky, M. V.; Mori, T.; Yang, C.; Ko, Y. H.; Selvapalam, N.; Kim, H.; Sobransingh, D.; Kaifer, A. E.; Liu, S.; Isaacs, L.; Chen, W.; Moghaddam, S.; Gilson, M. K.; Kim, K.; Inoue, Y. Proc. Natl. Acad. Sci. U.S.A. 2007, 104 (52) 20737-20742
5. Lagona, J.; Mukhopadhyay, P.; Chakrabarti, S.; Isaacs, L. Angew. Chem., Int. Ed. Engl. 2005, 44 (31) 4844-4870
6. Jeon, Y. J.; Kim, S. Y.; Ko, Y. H.; Sakamoto, S.; Yamaguchi, K.; Kim, K. Org. Biomol. Chem. 2005, 3 (11) 2122-2125
7. Zhao, Y. J.; Buck, D. P.; Morris, D. L.; Pourgholami, M. H.; Day, A. I.; Collins, J. G. Org. Biomol. Chem. 2008, 6 (24) 4509-4515
8. Ma, D.; Hettiarachchi, G.; Nguyen, D.; Zhang, B.; Wittenberg, J. B.; Zavalij, P. Y.; Briken, V.; Isaacs, L. Nat. Chem. 2012, 4 (6) 503-510
9. Hettiarachchi, G.; Nguyen, D.; Wu, J.; Lucas, D.; Ma, D.; Isaacs, L.; Briken, V. PLoS One 2010, 5 (5) e10514
10. El-Barghouthi, M. I.; Assaf, K. I.; Rawashdeh, A. M. M. J. Chem. Theory Comput. 2010, 6 (4) 984-992
11. Chen, W.; Chang, C. E.; Gilson, M. K. Biophys. J. 2004, 87 (5) 3035-3049
12. Moghaddam, S.; Yang, C.; Rekharsky, M.; Ko, Y. H.; Kim, K.; Inoue, Y.; Gilson, M. K. J. Am. Chem. Soc. 2011, 133 (10) 3570-3581
13. Muddana, H. S.; Gilson, M. K. J. Chem. Theory Comput. 2012, 8 (6) 2023-2033
14. Baron, R.; Setny, P.; McCammon, J. A. J. Am. Chem. Soc. 2010, 132 (34) 12091-12097
15. Hummer, G. Nat. Chem. 2010, 2 (11) 906-907
16. Setny, P.; Baron, R.; McCammon, J. A. J. Chem. Theory Comput. 2010, 6 (9) 2866-2871
17. Wang, L.; Friesner, R. A.; Berne, B. J. Faraday Discuss. 2010, 146, 247-262; discussion pp 283-298, 395-401
18. Wang, L.; Berne, B. J.; Friesner, R. A. Proc. Natl. Acad. Sci. U. S. A. 2011, 108 (4) 1326-1330
19. Young, T.; Hua, L.; Huang, X.; Abel, R.; Friesner, R.; Berne, B. J. Proteins 2010, 78 (8) 1856-1869
20. Baron, R.; Setny, P.; McCammon, J. A., Hydrophobic Association and Vol.-Confined Water Molecules. In Methods & Principles in Medicinal Chemisty-Protein-Ligand Interactions; Gohlke, H., Ed.; Wiley-VCH: Weinheim, Germany, 2012; pp 145-170.
21. Moghaddam, S.; Inoue, Y.; Gilson, M. K. J. Am. Chem. Soc. 2009, 131 (11) 4012-4021
22. Jorgensen, W. L.; Chandrasekhar, J.; Madura, J. D.; Impey, R. W.; Klein, M. L. J. Chem. Phys. 1983, 79 (2) 926-935
23. Kairys, V.; Gilson, M. K. J. Comput. Chem. 2002, 23 (16) 1656-1670
24. Jeon, W. S.; Moon, K.; Park, S. H.; Chun, H.; Ko, Y. H.; Lee, J. Y.; Lee, E. S.; Samal, S.; Selvapalam, N.; Rekharsky, M. V.; Sindelar, V.; Sobransingh, D.; Inoue, Y.; Kaifer, A. E.; Kim, K. J. Am. Chem. Soc. 2005, 127 (37) 12984-12989
25. Wang, J. M.; Wolf, R. M.; Caldwell, J. W.; Kollman, P. A.; Case, D. A. J. Comput. Chem. 2004, 25 (9) 1157-1174
26. Wang, J. M.; Wang, W.; Kollman, P. A.; Case, D. A. J. Mol. Graphics Modell. 2006, 25 (2) 247-260
27. Bayly, C. I.; Cieplak, P.; Cornell, W. D.; Kollman, P. A. J. Phys. Chem. 1993, 97 (40) 10269-10280
28. Cornell, W. D.; Cieplak, P.; Bayly, C. I.; Kollman, P. A. J. Am. Chem. Soc. 1993, 115 (21) 9620-9631
29. Case, D. A.; Cheatham, T. E., III; Darden, T.; Gohlke, H.; Luo, R.; Merz, K. M., Jr.; Onufriev, A.; Simmerling, C.; Wang, B.; Woods, R. J. J. Comput. Chem. 2005, 26 (16) 1668-1688
30. Fajer, M.; Baron, R.; de Oliveira, C. A. F.; Rogers, K.; Ortiz-Sanchez, J. M.; Wereszczynski, J.; Steinbrecher, T.; Walker, R. C.; McCammon, J. A. Manuscript in preparation.
31. Grest, G. S.; Kremer, K. Phys. Rev. A 1986, 33 (5) 3628-3631
32. Pastor, R. W.; Brooks, B. R.; Szabo, A. Mol. Phys. 1988, 65 (6) 1409-1419
33. Kirkwood, J. G. J. Chem. Phys. 1935, 3, 300-313
34. Zacharias, M.; Straatsma, T. P.; McCammon, J. A. J. Chem. Phys. 1994, 100 (12) 9025-9031
35. Steinbrecher, T.; Mobley, D. L.; Case, D. A. J. Chem. Phys. 2007, 127 (21) 214108
36. Allen, M. P.; Tildesley, D. J. Computer Simulations of Liquids; Oxford University Press: New York, 1989.
37. General, I. J. J. Chem. Theory Comput. 2010, 6 (8) 2520-2524
38. Gilson, M. K.; Given, J. A.; Bush, B. L.; McCammon, J. A. Biophys. J. 1997, 72 (3) 1047-1069
39. Hamelberg, D.; McCammon, J. A. J. Am. Chem. Soc. 2004, 126 (24) 7683-7689
40. Lawrenz, M.; Baron, R.; Wang, Y.; McCammon, J. A. J. Chem. Theory Comput. 2011, 7 (7) 2224-2232
41. Vega, C.; Abascal, J. L. Phys. Chem. Chem. Phys. 2011, 13 (44) 19663-19688
42. Nguyen, C. N.; Kurtzman Young, T.; Gilson, M. K. J. Chem. Phys. 2012, 137 (4) 044101