On the role of chemical detail in simulating protein folding kinetics

Chemical Physics

Volumn 323, Issue 1, 2006, Pages 66-77

  Rhee, Young Min ^a   Pande, Vijay S ^a  

^a STANFORD UNIVERSITY   (United States)

Author keywords

Distributed computing; Molecular dynamics; Protein folding; Solvent model

Indexed keywords

EID: 33645406972     PISSN: 03010104     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.chemphys.2005.08.060     Document Type: Article

References (48)

1. C.D. Snow, E.J. Sorin, Y.M. Rhee, and V.S. Pande Annu. Rev. Biophys. Biomol. Struct. 34 2005 43
2. A.R. Fersht, and V. Daggett Cell 108 2002 573
3. F.B. Sheinerman, and C.L. Brooks J. Mol. Biol. 278 1998 439
4. J.E. Shea, and C.L. Brooks Annu. Rev. Phys. Chem. 52 2001 499
5. E. Lindahl, B. Hess, and D. van der Spoel J. Mol. Model. 7 2001 306
6. M. Shirts, and V.S. Pande Science 290 2000 1903
7. V.S. Pande, I. Baker, J. Chapman, S.P. Elmer, S. Khaliq, S.M. Larson, Y.M. Rhee, M.R. Shirts, C.D. Snow, E.J. Sorin, and B. Zagrovic Biopolymers 68 2003 91
8. Y.M. Rhee, E.J. Sorin, G. Jayachandran, E. Lindahl, and V.S. Pande Proc. Natl. Acad. Sci. USA 101 2004 6456
9. G. Jayachandran, V. Vishal, V.S. Pande, in submission.
10. M.R. Shirts, and V.S. Pande J. Chem. Phys. 122 2005 134508
11. B.D. Bursulaya, and C.L. Brooks J. Phys. Chem. B 104 2000 12378
12. R.H. Zhou, and B.J. Berne Proc. Natl. Acad. Sci. USA 99 2002 12777
13. R.H. Zhou Proteins 53 2003 148
14. M.R. Shirts, J.W. Pitera, W.C. Swope, and V.S. Pande J. Chem. Phys. 119 2003 5740
15. M. Feig, A. Onufriev, M.S. Lee, W. Im, D.A. Case, and C.L. Brooks J. Comput. Chem. 25 2004 265
16. P.G. Bolhuis, D. Chandler, C. Dellago, and P.L. Geissler Annu. Rev. Phys. Chem. 53 2002 291
17. V.S. Pande, A.Y. Grosberg, T. Tanaka, and D.S. Rokhsar Curr. Opin. Struct. Biol. 8 1998 68
18. R. Du, V.S. Pande, A.Y. Grosberg, T. Tanaka, and E.S. Shakhnovich J. Chem. Phys. 108 1998 334
19. Y.M. Rhee, and V.S. Pande J. Phys. Chem. B 109 2005 6780
20. A. Ma, and A.R. Dinner J. Phys. Chem. B 109 2005 6769
21. C.W. Gardiner Handbook of Stochastic Methods 1985 Springer Berlin
22. G. Hummer J. Chem. Phys. 120 2004 516
23. M.D. Struthers, R.P. Cheng, and B. Imperiali Science 271 1996 342
24. M. Struthers, J.J. Ottesen, and B. Imperiali Fold. Des. 3 1998 95
25. A.E. Garcia, and K.Y. Sanbonmatsu Proc. Natl. Acad. Sci. USA 99 2002 2782
26. W.D. Cornell, P. Cieplak, C.I. Barly, I.R. Gould, K.M. Merz, D.M. Ferguson, D.C. Spellmeyer, T. Fox, J. Caldwell, and P.A. Kollman J. Am. Chem. Soc. 117 1995 5179
27. W.L. Jorgensen, J. Chandrasekhar, J.D. Madura, R.W. Impey, and M.L. Klein J. Chem. Phys. 79 1983 926
28. L.L. Chavez, J.N. Onuchic, and C. Clementi J. Am. Chem. Soc. 126 2004 8426
29. H.J.C. Berendsen, J.P.M. Postma, W.F. van Gunsteren, A. Dinola, and J.R. Haak J. Chem. Phys. 81 1984 3684
30. M. Neumann, and O. Steinhauser Mol. Phys. 39 1980 437
31. B. Hess, H. Bekker, H.J.C. Berendsen, and J.G.E.M. Fraaije J. Comput. Chem. 18 1997 1463
32. J.W. Ponder TINKER, Software Tools for Molecular Design 2000 Department of Biochemistry and Molecular Biophysics, Washington University St. Louis
33. D. Qiu, P.S. Shenkin, F.P. Hollinger, and W.C. Still J. Phys. Chem. A 101 1997 3005
34. B. Hess J. Chem. Phys. 116 2002 209
35. M. Tachiya J. Chem. Phys. 69 1978 2375
36. D. Chandler Nature 417 2002 491
37. P.R. ten Wolde, and D. Chandler Proc. Natl. Acad. Sci. USA 99 2002 6539
38. H. Taketomi, Y. Ueda, and N. Go Int. J. Peptide Protein Res. 7 1975 445
39. T. Head-Gordon, and S. Brown Curr. Opin. Struct. Biol. 13 2003 160
40. G. Hummer, S. Garde, A.E. Garcia, M.E. Paulaitis, and L.R. Pratt Proc. Natl. Acad. Sci. USA 95 1998 1552
41. M.S. Cheung, A.E. Garcia, and J.N. Onuchic Proc. Natl. Acad. Sci. USA 99 2002 685
42. J. Karanicolas, and C.L. Brooks Protein Sci. 11 2002 2351
43. J.E. Shea, J.N. Onuchic, and C.L. Brooks Proc. Natl. Acad. Sci. USA 99 2002 16064
44. A. Cavalli, M. Vendruscolo, and E. Paci Biophys. J. 88 2005 3158
45. C.D. Snow, N. Nguyen, V.S. Pande, and M. Gruebele Nature 420 2002 102
46. P.L. Geissler, C. Dellago, and D. Chandler J. Phys. Chem. B 103 1999 3706
47. P.G. Bolhuis, C. Dellago, and D. Chandler Proc. Natl. Acad. Sci. USA 97 2000 5877
48. C. Clementi, H. Nymeyer, and J.N. Onuchic J. Mol. Biol. 298 2000 937