Monte Carlo simulations of polyalanine using a reduced model and statistics-based interaction potentials

Journal of Chemical Physics

Volumn 122, Issue 2, 2005, Pages

  Van Giessen, Alan E ^a   Straub, John E ^a  

^a Boston University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

CHAIN LENGTH; INTERACTION POTENTIAL; ORIENTATIONS; POLYALANINE;

AMINO ACIDS; ATOMS; HYDROGEN BONDS; MATHEMATICAL MODELS; POLYPEPTIDES; STATISTICAL METHODS;

MONTE CARLO METHODS;

PEPTIDE; POLYALANINE;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; MONTE CARLO METHOD; TEMPERATURE;

COMPUTER SIMULATION; MODELS, MOLECULAR; MONTE CARLO METHOD; PEPTIDES; TEMPERATURE;

EID: 34548105157     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.1833354     Document Type: Article

References (35)

1. H. M. Berman, J. Westbrook, Z. Feng, G. Gilliland, T. N. Bhat, H. Weissig, I. N. Shindyalov, and P. E. Bourne, Nucleic Acids Res. 28, 235 (2000).
2. S. Tanaka and H. A. Scheraga, Macromolecules 9, 945 (1976).
3. J. Lee, A. Liwo, and H. A. Scheraga, Proc. Natl. Acad. Sci. U.S.A. 96, 2025 (1999).
4. S. Miyazawa and R. L. Jernigan, Proteins 34, 49 (1999).
5. A. Godzik, A. Kolinski, and J. Skolnick, Protein Sci. 4, 2107 (1995).
6. M. J. Sippl, J. Mol. Biol. 213, 859 (1990).
7. M. J. Sippl, Curr. Opin. Struct. Biol. 5, 229 (1995).
8. M. Betancourt and D. Thirumalai, Protein Sci. 8, 361 (1999).
9. M. Vendruscolo and E. Domany, J. Chem. Phys. 109, 11101 (1998).
10. A. Ben-Naim, J. Chem. Phys. 107, 3698 (1997).
11. D. Tobi and R. Elber, Proteins 41, 40 (2000).
12. D. Tobi, G. Shafran, N. Linial, and R. Elber, Proteins 40, 71 (2000).
13. J. Meller and R. Elber, Proteins 45, 241 (2001).
14. J. Meller, M. Wagner, and R. Elber, J. Comput. Chem. 23, 111 (2002).
15. D. Gatchell, S. Dennis, and S. Vajda, Proteins 41, 518 (2000).
16. N.-V. Buchete and J. E. Straub, J. Chem. Phys. 118, 7658 (2003).
17. N.-V. Buchete, J. E. Straub, and D. Thirumalai, Polymer 45, 597 (2004).
18. N.-V. Buchete, J. E. Straub, and D. Thirumalai, J. Mol. Graphics Modell. 22, 441 (2004).
19. S. Takada, Z. Luthey-Schulten, and P. G. Wolynes, J. Chem. Phys. 110, 11616 (1999).
20. A. Voegler Smith and C. K. Hall, J. Mol. Biol. 312, 187 (2001).
21. B. Honig and F. E. Cohen, Folding Des. 1, R17 (1996).
22. N.-V. Buchete, J. E. Straub, and D. Thirumalai, Protein Sci. 13, 862 (2004).
23. J. Shimada, E. L. Kussell, and E. I. Shakhnovich, J. Mol. Biol. 308, 79 (2001).
24. J. Shimada and E. I. Shakhnovich, Proc. Natl. Acad. Sci. U.S.A. 99, 11175 (2002).
25. G. Favrin, A. Irbäck, and F. Sjunnesson, J. Chem. Phys. 114, 8154 (2001).
26. J. P. Ulmschneider and W. J. Jorgensen, J. Chem. Phys. 118, 4261 (2003).
27. R. H. Swendon and J.-S. Wang, Phys. Rev. Lett. 57, 2607 (1986).
28. K. Hukushima and K. Nemoto, J. Phys. Soc. Jpn. 65, 1604 (1996).
29. Y. Sugita and Y. Okamoto, Chem. Phys. Lett. 329, 261 (2000).
30. C. R. Cantor and P. R. Schimmel, Biophysical Chemistry; Part I (Freedman, New York, 1980).
31. T. Veitshans, D. Klimov, and D. Thirumalai, Folding Des. 1, 1 (1996).
32. S. Kumar, D. Bouzida, R. H. Swendsen, P. A. Kollman, and J. M. Rosenberg, J. Comput. Chem. 13, 1011 (1992).
33. U. H. E. Hansmann and Y. Okamoto, J. Chem. Phys. 110, 1267 (1999).
34. B. H. Zimm and J. K. Bragg, J. Chem. Phys. 31, 526 (1959).
35. Y. Chen, Q. Zhang, and J. Ding, J. Chem. Phys. 120, 3467 (2004).