Evaluation of configurational entropy methods from peptide folding-unfolding simulation

Journal of Physical Chemistry B

Volumn 111, Issue 49, 2007, Pages 13807-13813

  Li, Da Wei ^a   Khanlarzadeh, Mina ^a   Wang, Jinbu ^a,c   Huo, Shuanghong ^a   Brüschweiler, Rafael ^b  

^a CLARK UNIVERSITY   (United States)

^b FLORIDA STATE UNIVERSITY   (United States)

^c NATIONAL CANCER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; FREE ENERGY; FUNCTION EVALUATION; PEPTIDES;

FREE ENERGY SURFACE; ROOT-MEAN-SQUARE DEVIATION (RMSD);

ENTROPY;

EID: 38049123863     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp075220e     Document Type: Article

References (39)

1. Meirovitch, H. Curr. Opin. Struct. Biol. 2007, 17, 181.
2. Lazaridis, T.; Karplus, M. Curr. Opin. Struct. Biol. 2000, 10, 139.
3. Liwo, A.; Khalili, M.; Scheraga, H. A. Proc. Natl. Acad. Sci. U.S.A. 2005, 102, 2362.
4. Bicout, D. J.; Szabo, A. Protein Sci. 2000, 9, 452.
5. Galzitskaya, O. V.; Surin, A. K.; Nakamura, H. Protein Sci. 2000, 9, 580.
6. Frenkel, D.; Smit, B. Understanding Molecular Simulation: From Algorithms to Applications, 2nd ed.; Academic Press: San Diego, CA, 2002.
7. Go, N.; Scheraga, H. A. Macromolecules 1976, 9, 535.
8. Karplus, M.; Kushick, J. N. Macromolecules 1981, 14, 325.
9. Di Nola, A.; Berendsen, H. J. C.; Edholm, O. Macromolecules 1984, 17, 2044.
10. Edholm, O.; Berendsen, H. J. C. Mol. Phys. 1984, 51, 1101.
11. Schlitter, J. Chem. Phys. Lett. 1993, 215, 617.
12. Schafer, H.; Mark, A. E.; van Gunsteren, W. F. J. Chem. Phys. 2000, 113, 7809.
13. Andricioaei, L.; Karplus, M. J. Chem. Phys. 2001, 115, 6289.
14. Hnizdo, V.; Fedorowicz, A.; Singh, H.; Demchuk, E. J. Comput. Chem. 2003, 24, 1172.
15. Cheluvaraja, S.; Meirovitch, H. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 9241.
16. Cheluvaraja, S.; Meirovitch, H. J. Phys. Chem. B 2005, 109, 21963.
17. Cheluvaraja, S.; Meirovitch, H. J. Chem. Phys. 2005, 122, 54903.
18. Darian, E.; Hnizdo, V.; Fedorowicz, A.; Singh, H.; Demchuk, E. J. Comput. Chem. 2005, 26, 651.
19. Cheluvaraja, S.; Meirovitch, H. J. Chem. Phys. 2006, 125, 24905.
20. Wang, J.; Briischweiler, R. J. Chem. Theory Comput. 2006, 2, 18.
21. Hnizdo, V.; Darían, E.; Fedorowicz, A.; Demchuk, E.; Li, S.; Singh, H. J. Comput. Chem. 2007, 28, 655.
22. van Aalten, D. M. D.; de Groot, B. L.; Findlay, J. B. C.; Berendsen, H. J. C.; Amadei, A. J. Comput. Chem. 1997, 18, 169.
23. Abseher, R.; Nilges, M. J. Mol. Biol. 1998, 279, 911.
24. Mu, Y.; Nguyen, P. H.; Stock, G. Proteins 2005, 58, 45.
25. Schafer, H.; Daura, X.; Mark, A. E.; van Gunsteren, W. F. Proteins: Struct., Funct., Genet. 2001, 43, 45.
26. Chang, C. E.; Chen, W.; Gilson, M. K. J. Chem. Theory Comput. 2005, 1, 1017.
27. Krivov, S. V.; Karplus, M. Proc. Natl. Acad. Sci. U.S.A. 2004, 101, 14766.
28. Brooks, B. R.; Bruccoleri, R. E.; Olafson, B. D.; States, D. J.; Swaminathan, S.; Karplus, M. J. Comput. Chem. 1983, 4, 187.
29. Lazaridis, T.; Karplus, M. Proteins 1999, 35, 133.
30. Lazaridis, T.; Karplus, M: Science 1997, 278, 1928.
31. Dinner, A. R.; Lazaridis, T.; Karplus, M. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 9068.
32. Yang, H.; Wu, H.; Li, D.; Han, L.; Huo, S. J. Chem. Theory Comput. 2007, 3, 17.
33. Daura, X.; Gademann, K.; Jaun, B.; Seebach, D.; van Gunsteren, W. F.; Mark, A. E. Angew. Chem., Int. Ed. 1999, 38, 236.
34. Li, D. W.; Han, L.; Huo, S. J. Phys. Chem. B 2007, 111, 5425.
35. Prompers, J. J.; Brüschweiler, R. J. Phys. Chem. B 2000, 104, 11416.
36. Akke, M.; Brüschweiler, R.; Palmer, A. G. J. Am. Chem. Soc. 1993, 115, 9832.
37. Marlow, M. S.; Wand, A. J. Biochemistry 2006, 45, 8732.
38. Yang, D.; Kay, L. E. J. Mol. Biol. 1996, 263, 369.
39. Pettersen, E. F.; Goddard, T. D.; Huang, C. C.; Couch, G. S.; Greenblatt, D. M.; Meng, E. C.; Ferrin, T. E. J. Comput. Chem. 2004, 25, 1605.