Tackling the protein folding problem by a generalized-ensemble approach with Tsallis statistics

Brazilian Journal of Physics

Volumn 29, Issue 1, 1999, Pages 187-198

  Hansmann, Ulrich H E ^a   Okamoto, Yuko ^b,c  

^a MICHIGAN TECHNOLOGICAL UNIVERSITY   (United States)

^b INSTITUTE FOR MOLECULAR SCIENCE   (Japan)

^c GRADUATE UNIVERSITY FOR ADVANCED STUDIES   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0033243015     PISSN: 01039733     EISSN: None     Source Type: Journal    
DOI: 10.1590/S0103-97331999000100017     Document Type: Review

References (50)

1. [1] S. Kirkpatrick, C.D. Gelatt, Jr., and M.P. Vecchi, Science 220, 671 (1983).
2. [2] B.A. Berg and T. Neuhaus, Phys. Lett. B267, 249 (1991); Phys. Rev. Lett. 68, 9 (1992).
3. [2] B.A. Berg and T. Neuhaus, Phys. Lett. B267, 249 (1991); Phys. Rev. Lett. 68, 9 (1992).
4. [3] B.A. Berg, Int. J. Mod. Phys. C3, 1083 (1992).
5. [4] U.H.E. Hansmann and Y. Okamoto, J. Comp. Chem. 14, 1333 (1993).
6. [5] A.P. Lyubartsev, A.A. Martinovski, S.V. Shevkunov, and P.N. Vorontsov-Velyaminov, J. Chem. Phys. 96, 1776 (1992).
7. [6] E. Marinari and G. Parisi, Europhys. Lett. 19, 451 (1992).
8. [7] B. Hesselbo and R.B. Stinchcombe. Phys. Rev. Lett. 74, 2151 (1995).
9. [8] U.H.E. Hansmann and Y. Okamoto, J. Comp.Chem. 18, 920 (1997).
10. [9] U.H.E. Hansmann, Y. Okamoto and F. Eisenmenger, Chem. Phys. Lett. 259, 321 (1996).
11. [10] N. Nakajima, H. Nakamura and A. Kidera, J. Phys. Chem. 101, 817 (1997).
12. [11] C. Bartels and M. Karplus, J. Phys. Chem. B 102, 865 (1998).
13. [12] C. Tsallis, J. Stat. Phys. 52, 479 (1988).
14. [13] U.H.E. Hansmann and Y. Okamoto, Phys. Rev. E56, 2228 (1997).
15. [14] U.H.E. Hansmann, F. Eisenmenger, and Y. Okamoto, Chem. Phys. Lett. 297, 374 (1998).
16. [15] F.A. Momany, R.F. McGuire, A.W. Burgess, and H.A. Scheraga, J. Phys. Chem. 79, 2361 (1975); G. Némethy, M.S. Pottle, and H.A. Scheraga, J. Phys. Chem. 87, 1883 (1983); M.J. Sippl. G. Némethy, and H.A. Scheraga, J. Phys. Chem. 88, 6231 (1984).
17. [15] F.A. Momany, R.F. McGuire, A.W. Burgess, and H.A. Scheraga, J. Phys. Chem. 79, 2361 (1975); G. Némethy, M.S. Pottle, and H.A. Scheraga, J. Phys. Chem. 87, 1883 (1983); M.J. Sippl. G. Némethy, and H.A. Scheraga, J. Phys. Chem. 88, 6231 (1984).
18. [15] F.A. Momany, R.F. McGuire, A.W. Burgess, and H.A. Scheraga, J. Phys. Chem. 79, 2361 (1975); G. Némethy, M.S. Pottle, and H.A. Scheraga, J. Phys. Chem. 87, 1883 (1983); M.J. Sippl. G. Némethy, and H.A. Scheraga, J. Phys. Chem. 88, 6231 (1984).
19. [16] H. Kawai, Y. Okamoto, M. Fukugita, T. Nakazawa, and T. Kikuchi, Chem. Lett. 1991, 213 (1991); Y. Okamoto, M. Fukugita, T. Nakazawa, and H. Kawai, Protein Eng. 4, 639 (1991).
20. [16] H. Kawai, Y. Okamoto, M. Fukugita, T. Nakazawa, and T. Kikuchi, Chem. Lett. 1991, 213 (1991); Y. Okamoto, M. Fukugita, T. Nakazawa, and H. Kawai, Protein Eng. 4, 639 (1991).
21. [17] The program SMG was written by F. Eisenmenger.
22. [18] N. Metropolis, A.W. Rosenbluth, M.N. Rosenbluth, A.H. Teller, and E. Teller, J. Chem. Phys. 21. 1087 (1953).
23. [19] S. Geman and D. Geman. IEEE Trans. Patt Anal. Mach. Intel 6, 721 (1984).
24. [20] U.H.E. Hansmann and Y. Okamoto, J. Phys. Soc. Jpn. 63, 3945 (1994); Physica A 212, 415 (1994).
25. [20] U.H.E. Hansmann and Y. Okamoto, J. Phys. Soc. Jpn. 63, 3945 (1994); Physica A 212, 415 (1994).
26. [21] S.R. Wilson, W. Gui, J.W. Moskowitz, and K.E. Schmidt, Tetrahedron Lett. 29, 4373 (1988).
27. [22] H. Kawai, T. Kikuchi, and Y. Okamoto, Protein Eng. 3, 85 (1989).
28. [23] C. Wilson and S. Doniach, Proteins 6, 193 (1989).
29. [24] A.T. Brünger, J. Mol. Biol. 203, 803 (1988).
30. [25] M. Nilges, G.M. Clore, and A.M. Gronenborn, FEBS Lett. 229, 317 (1988).
31. [26] M. Pellegrini, N. Grønbech-Jensen, and S. Doniach, Physica A 239, 244 (1997).
32. [27] M. Kinoshita, Y. Okamoto, F. Hirata, J. Am. Chem. Soc. 120, 1855 (1998).
33. [28] L. Carlacci, J. Comp-Aided Mol. Des. 12, 195 (1998).
34. [29] Y. Okamoto, M. Masuya, M. Nabeshima and T. Nakazawa, Chem. Phys. Lett. 299, 17 (1999).
35. [30] H. Szu and R. Hartley, Phys. Lett. A122, 157 (1987).
36. [31] D.A. Stariolo and C. Tsallis, in Annual Reviews of Computational Physics II, edited by D. Stauffer (World Scientific, Singapore, 1995). p. 343.
37. [32] T.J.P. Penna, Phys. Rev. E 51, R1 (1995).
38. [33] I. Andricioaei and J.E. Straub, Phys. Rev. E 53, R3055 (1996).
39. [34] U.H.E. Hansmann, Physica A 242, 250 (1997).
40. [35] A.M. Ferrenberg and R.H. Swendsen, Phys. Rev. Lett. 61, 2635 (1988); ibid. 63, 1658(E) (1989).
41. [35] A.M. Ferrenberg and R.H. Swendsen, Phys. Rev. Lett. 61, 2635 (1988); ibid. 63, 1658(E) (1989).
42. [36] D.A. Stariolo, Phys. Lett. A185, 262 (1994).
43. [37] I. Andricioaei and J.E. Straub, J. Chem. Phys. 107, 9117 (1997).
44. [38] G. Parisi and Y.-S. Wu, Sci. Sin. 24, 483 (1981).
45. [39] S. Duane, A.D. Kennedy, B.J. Pendleton, and D. Roweth. Phys. Lett. B195, 216 (1987). references given in the erratum.
46. [40] Y. Okamoto, T. Kikuchi, and H. Kawai, Chem. Lett. 1992, 1275 (1992).
47. [41] U.H.E. Hansmann, M. Masuya, and Y. Okamoto, Proc. Natl. Acad. Sci. USA 94, 10652 (1997).
48. [42] M. Masuya, in preparation.
49. [43] F. Eisenhaber, P. Lijnzaad, P. Argos, C. Sander, and M. Scharf, J. Comp. Chem. 16, 273 (1995).
50. [44] U.H.E. Hansmann, Y. Okamoto, and J.N. Onuchic, "The folding funnel landscape for the peptide Metenkephalin," Proteins: Structure, Function, and Genetics (1999), in press.