Analyzing the robustness of the MM/PBSA free energy calculation method: Application to DNA conformational transitions

Journal of Computational Chemistry

Volumn 32, Issue 7, 2011, Pages 1431-1440

  Brice, Allyn R ^a   Dominy, Brian N ^a  

^a CLEMSON UNIVERSITY   (United States)

Author keywords

A form; amber; B form; CHARMM; DNA; free energy; generalized born; MM PBSA

Indexed keywords

A-FORM; B-FORM; CHARMM; GENERALIZED BORN; MM-PBSA;

AMBER; DNA; IONIC STRENGTH; MOLECULAR BIOLOGY; NUCLEIC ACIDS; SOLVENTS;

FREE ENERGY;

DNA; SOLVENT;

ARTICLE; CHEMISTRY; CONFORMATION; MOLECULAR DYNAMICS; SURFACE PROPERTY;

DNA; MOLECULAR DYNAMICS SIMULATION; NUCLEIC ACID CONFORMATION; SOLVENTS; SURFACE PROPERTIES;

EID: 79953003050     PISSN: 01928651     EISSN: 1096987X     Source Type: Journal    
DOI: 10.1002/jcc.21727     Document Type: Article

References (45)

1. Saenger, W., Principles of Nucleic Acid Structure, New York: Springer-Verlag, 1984.
2. Cheatham, T. E., Curr Opin Struct Biol 2004, 14, 360.
3. Vargason, J. M.,;, Henderson, K.,;, Ho, P. S., Proc Natl Acad Sci USA 2001, 98, 7265.
4. Yang, L.,;, Pettitt, B. M., J Phys Chem 1996, 100, 2564.
5. Jose, D.,;, Porschke, D., J Am Chem Soc 2005, 127, 16120.
6. Lu, X.-J.,;, Olson, W. K., Nucleic Acids Res 2003, 31, 5108.
7. Srinivasan, J.,;, Cheatham, T. E., III,;, Cieplak, P.,;, Kollman, P. A.,;, Case, D. A., J Am Chem Soc 1998, 120, 9401.
8. McConnell, K. J.,;, Beveridge, D. L., J Mol Biol 2000, 304, 803.
9. Cheatham, T. E.,;, Crowley, M. F.,;, Fox, T.,;, Kollman, P. A., Proc Natl Acad Sci USA 1997, 94, 9626.
10. Minchenkova, L. E.,;, Shchelkina, A. K.,;, Chernov, B. K.,;, Ivanov, V. I., J Biomol Struct Dyn 1986, 4, 463.
11. Leslie, A. G. W.,;, Arnott, S.,;, Chandrasekaran, R.,;, Ratliff, R. L., J Mol Biol 1980, 143, 49.
12. Saenger, W.,;, Hunter, W. N.,;, Kennard, O., Nature 1986, 324, 385-388.
13. Lu, X.-J.,;, Shakked, Z.,;, Olson, W. K., J Mol Biol 2000, 300, 819.
14. Arya, D. P., Topics in Current Chemistry 2005; Vol. 253; (DNA Binders and Related Subjects), pp. 149-178.
15. Torrie, G. M.,;, Valleau, J. P., J Chem Phys 1977, 66, 1402-1408.
16. Leach, A. R., Molecular Modelling: Principles and Applications, New York: Prentice Hall, 2000.
17. Frenkel, D., Smit, B., Understanding Molecular Simulation: From Algorithms to Applications, San Diego: Academic Press, 1996.
18. Gilson, M. K.,;, Given, J. A.,;, Bush, B. L.,;, McCammon, J. A., Biophysical J 1997, 72, 1047-1069.
19. Kollman, P., Chemical Reviews, Vol. 93; Washington, DC, United States, 1993; pp. 2395-2417.
20. Lazaridis, T.,;, Masunov, A.,;, Gandolfo, F., Proteins: Struct Funct Genet 2002, 47, 194.
21. Weis, A.,;, Katebzadeh, K.,;, Soederhjelm, P.,;, Nilsson, I.,;, Ryde, U., JMed Chem 2006, 49, 6596.
22. Swanson, J. M. J.,;, Henchman, R. H.,;, McCammon, J. A., Biophysical J 2004, 86 (1, Pt. 1), 67.
23. Luo, H.,;, Sharp, K., Proc Natl Acad Sci USA 2002, 99, 10399.
24. Kollman, P. A.,;, Massova, I.,;, Reyes, C.,;, Kuhn, B.,;, Huo, S.,;, Chong, L.,;, Lee, M.,;, Lee, T.,;, Duan, Y.,;, Wang, W.,;, Donini, O.,;, Cieplak, P.,;, Srinivasan, J.,;, Case, D. A.,;, Cheatham, T. E., III., Acc Chem Res 2000, 33, 889-897.
25. Lee, M. S.,;, Olson, M. A., Biophysical J 2006, 90, 864.
26. Banavali, N. K.,;, Roux, B., J Am Chem Soc 2005, 127, 6866.
27. Cornell, W. D.,;, Cieplak, P.,;, Bayly, C. I.,;, Gould, I. R.,;, Merz, K. M., Jr.,;, Ferguson, D. M.,;, Spellmeyer, D. C.,;, Fox, T.,;, Caldwell, J. W.,;, Kollman, P. A., J Am Chem Soc 1995, 117, 5179.
28. Foloppe, N.,;, Mackerell, A. D., J Comput Chem 2000, 21, 86.
29. Drew, H. R.,;, Wing, R. M.,;, Takano, T.,;, Broka, C.,;, Tanaka, S.,;, Itakura, K.,;, Dickerson, R. E., Proc Natl Acad Sci USA 1981, 78, 2179.
30. Brooks, B. R.,;, Bruccoleri, R. E.,;, Olafson, B. D.,;, States, D. J.,;, Swaminathan, S.,;, Karplus, M., J Comput Chem 1983, 4, 187-217.
31. Darden, T.,;, York, D.,;, Pedersen, L., J Chem Phys 1993, 98, 10089.
32. Cremer, D.,;, Pople, J. A., J Am Chem Soc 1975, 97, 1354.
33. Andersen, H. C., J Chem Phys 1980, 72, 2384.
34. Ryckaert, J. P.,;, Ciccotti, G.,;, Berendsen, H. J. C., J Comput Phys 1977, 23, 327.
35. Im, W.,;, Lee, M. S.,;, Brooks, C. L., III., J Comput Chem 2003, 24, 1691.
36. Chocholousova, J.,;, Feig, M., J Comput Chem 2006, 27, 719.
37. Chocholousova, J.,;, Feig, M., J Phys Chem B 2006, 110, 17240.
38. Adelman, S. A.,;, Doll, J. D., J Chem Phys 1976, 64, 2375.
39. Wahl, M. C.,;, Rao, S. T.,;, Sundaralingam, M., Biophys J 1996, 70, 2857.
40. Sands, Z. A.,;, Laughton, C. A., J Phys Chem B 2004, 108, 10113.
41. Duong, T.,; Zakrzewska, K. J Comput Chem 1997, 18, 796.
42. Lee, M.,; Van der Vegt, NFA. J Chem Theory Comput 2007, 3, 194.
43. Qian, H.,;, Hopfield, J. J., J Chem Phys 1996, 105, 9292.
44. Bertonati, C.,;, Honig, B.,;, Alexov, E., Biophys J 2007, 92, 1891.
45. Srinivasan, J.,;, Trevathan, M. W.,;, Beroza, P.,;, Case, D. A., Theor Chem Acc 1999, 101, 426.