Temperature weighted histogram analysis method, replica exchange, and transition paths

Journal of Physical Chemistry B

Volumn 109, Issue 14, 2005, Pages 6722-6731

  Gallicchio, Emilio ^a   Andrec, Michael ^a   Felts, Anthony K ^a   Levy, Ronald M ^a  

^a RUTGERS UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HISTOGRAM ANALYSIS; MEAN FORCE; MOLECULAR DYNAMICS SIMULATIONS; SECONDARY STRUCTURES;

COMPUTER SIMULATION; CONFORMATIONS; LARGE SCALE SYSTEMS; POLYPEPTIDES; PROTEINS; SEPARATION; SOLUTIONS; STATISTICAL METHODS;

MOLECULAR DYNAMICS;

PEPTIDE; PROTEIN;

ALGORITHM; ARTICLE; BAYES THEOREM; CHEMISTRY; COMPUTER SIMULATION; CONFORMATION; METHODOLOGY; MONTE CARLO METHOD; PHYSICAL CHEMISTRY; PROTEIN CONFORMATION; PROTEIN MOTIF; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; STATISTICAL MODEL; TEMPERATURE; THERMODYNAMICS;

ALGORITHMS; AMINO ACID MOTIFS; BAYES THEOREM; CHEMISTRY, PHYSICAL; COMPUTER SIMULATION; LIKELIHOOD FUNCTIONS; MOLECULAR CONFORMATION; MONTE CARLO METHOD; PEPTIDES; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTEINS; TEMPERATURE; THERMODYNAMICS;

EID: 17444366185     PISSN: 15206106     EISSN: None     Source Type: Journal    
DOI: 10.1021/jp045294f     Document Type: Article

References (58)

1. Elber, R.; Karplus, M. Chem. Phys. Lett. 1987, 139, 375-380.
2. Bolhuis, P. G.; Chandler, D.; Dellago, C.; Geissler, P. L. Annu. Rev. Phys. Chem. 2002, 53, 291.
3. Bolhuis, P. G. Proc. Natl. Acad. Sci. U.S.A. 2003, 100, 12129-12134.
4. Eastman, P.; Grønbech-Jensen. N.; Doniach, S. J. Chem. Phys. 2001, 114, 3823-3841.
5. Onuchik. J. N.; Luthey-Schulten, Z.; Wolynes, P. G. Annu. Rev. Phys. Chem. 1997, 48, 545-600.
6. Kumar, S.; Ma, B.; Tsai, C.-J.; Sinha, N.; Nussinov, R. Protein Sci. 2000, 9, 10-19.
7. Onuchic, J. N.; Wolynes, P. G. Curr. Opin. Struct. Biol. 2004, 14, 70-75.
8. Sugita, Y.; Okamoto, Y. Chem. Phys. Lett. 1999, 314, 141-151.
9. García, A. E.; Sanbonmatsu, K. Y. Proteins: Struct. Funct. Genet. 2001, 42, 345-354.
10. Zhou, R.; Berne, B. J.; Germain, R. Proc. Natl. Acad. Sci. U.S.A. 2001, 98, 14931-14936.
11. Felts, A. K.; Harano, Y.; Gallicchio, E.; Levy, R. M. Proteins 2004, 56, 310-321.
12. Ferrenberg, A. M.; Swendsen, R. H. Phys. Rev. Lett. 1989, 63, 1195-1198.
13. Kumar, S.; Bouzida, D.; Swendsen, R. H.; Kollman, P. A.; Roscnberg, J. M. J. Comput. Chem. 1992, 13, 1011-1021.
14. Roux, B. Comput. Phys. Comm. 1995, 91, 275-282.
15. Sugita, Y.; Kitao, A.; Okamoto, Y. J. Chem. Phys. 2000, 113, 6042-6050.
16. Shea, J.-E.; Brooks, C. L., III Annu. Rev. Phys. Chem. 2001, 52, 499-535.
17. Ferrenberg, A. M.; Swendsen, R. H. Comput. Phys. 1989, Sept/Oct, 101-104.
18. Bartels, C.; Karplus, M. J. Comput. Chem. 1997, 18, 1450-1462.
19. Honda, S.; Kobayashi, N.; Munekata, E. J. Mol. Biol. 2000, 295, 269-278.
20. Blanco, F. J.; Rivas, G.; Semmo, L. Nat. Struct. Biol. 1994, 1, 584-590.
21. Muñoz, V.; Henry, E. R.; Hoftichter, J.; Eaton, W. A. Proc. Natl. Acad. Sci. U.S.A. 1998, 95, 5872-5879.
22. Kobayashi, N.; Honda, S.; Yoshii, H.; Munekata, E. Biochemistry 2000, 39, 6564-6571.
23. Dinner, A. R.; Lazaridis, T.; Karplus, M. Proc. Natl. Acad. Sci. U.S.A. 1999, 96, 9068-9073.
24. Kolinski, A.; Ilkowski. B.; Skolnick, J. Biophys. J. 1999, 77, 2942-2952.
25. Pande, V.; Rokhsar, D. S. Proc. Natl. Acad. Sci. U.S.A. 1999, 90, 9062-9067.
26. Roccatano, D.; Amadei, A.; Di Nola, A.; Berendsen, H. J. Protein Sci. 1999, 8, 2130-2143.
27. Ma, B.; Nussinov, R. J. Mol. Biol. 2000, 296, 1091-1104.
28. Zagrovic, B.; Sorin, E. J.; Pande, V. J. Mol. Biol. 2001, 313, 151-169.
29. Zhou, R.; Berne, B. J. Proc. Natl. Acad. Sci. U.S.A. 2002, 99, 12777-12782.
30. Zhou, Y.; Linhananta, A. Proteins: Struct. Funct. Genet. 2002, 47, 154-162.
31. Lee, J.; Shin, S. J. Phys. Chem. B 2002, 106, 8796-8802.
32. Tsai, J.; Levitt, M. Biophys. Chem. 2002, 101-102, 187-201.
33. Muñoz, V.; Thompson, P. A.; Hofrichter, J.; Eaton, W. A. Nature 1997, 390, 196-199.
34. Andrec, M.; Felts, A. K.; Gallicchio, E.; Levy, R. M. In preparation.
35. Hamada, D.; Segawa, S.; Goto, Y. Nat. Struct. Biol. 1996, 3, 868-873.
36. Kuwajima, K.; Yamaya. H.; Sugai, S. J. Mol. Biol. 1996, 264, 806-822.
37. Hamada, D.; Goto, Y. J. Mol. Biol. 1997, 269, 479-487.
38. Arai, M.; Ikura, T.; Semisotnov, G.; Kihara, H.; Amemiya, Y.; Kuwajima, K. J. Mol. Biol. 1998, 275, 149-162.
39. Forge, V.; Hoshino, M.; Kuwata, K.; Arai, M.; Kuwajima, K.; Batt, C. A.; Goto, Y. J. Mol. Biol. 2000, 296, 1039-1051.
40. Kuwata, K.; Shastry, R.; Cheng, H.; Hoshino, M.; Batt, C. A.; Goto, Y.; Roder, H. Nat. Struct. Biol. 2001, 8, 151-155.
41. Sivia, D. S. Data Analysis: A Bayesian Tutorial; Oxford University Press: Oxford, 1996.
42. De Bruijn, N. G. Asymptotic Methods in Analysis; Dover: New York, 1981.
43. Metropolis, N.; Rosenbluth, A. W.; Rosenbluth, M. N.; Teller, A. H.; Teller, E. J. Chem. Phys. 1953, 21, 1087-1091.
44. Hastings, W. K. Biometrika 1970, 57, 97-109.
45. Dellago, C.; Bolhuis, P. G.; Csajka, F. S.; Chandler, D. J. Chem. Phys. 1998, 108, 1964-1977.
46. Okzan, S. B.; Dill, K. A.; Behar, I. Protein Sci. 2002, 11, 1958-1970.
47. Okzan, S. B.; Dill, K. A.; Behar, I. Biopolymers 2003, 68, 35-46.
48. Chekmarev, D.; Ishida, T.; Levy, R. M. J. Phys. Chem. B 2004, 108, 19487-19495.
49. Evans, D. A.; Wales, D. J. J. Chem. Phys. 2004, 121, 1080-1090.
50. Kitchen, D. B.; Hirata, F.; D. A. Kofke, D. A.; Westbrook, J. D.; Yormush, M.; Levy, R. M. J. Comput. Chem. 1990, 11, 1169-1180.
51. Jorgensen, W. L.; Maxwell, D. S.; Tirado-Rives, J. J. Am. Chem. Soc. 1996, 118, 11225-11236.
52. Gallicchio, E.; Levy, R. M. J. Comput. Chem. 2004, 25, 479-499.
53. Qiu, D.; Shenkin, P. S.; Hollinger, F. P.; Still, W. C. J. Phys. Chem. A 1997, 101, 3005-3014.
54. Johnson, N. L.; Kotz, S. Distributions in Statistics: Continuous Multivariate Distributions; John Wiley & Sons: New York, 1972.
55. Gelfand, A. E.; Smith, A. F. M. J. Am. Stat. Assn. 1990, 85, 398-409.
56. Bratley, P.; Fox, B. L.; Schrage, L. E. A Guide to Simulation; Springer-Verlag: New York, 1987.
57. Frishman, D.; Argos, P. Proteins 1995, 23, 566-579.
58. Humphrey, W.; Dalke, A.; Schulten, K. J. Mol. Graphics 1996, 14, 33-38.