Efficiently explore the energy landscape of proteins in molecular dynamics simulations by amplifying collective motions

Journal of Chemical Physics

Volumn 119, Issue 7, 2003, Pages 4005-4017

  He, Jianbin ^a   Zhang, Zhiyong ^a   Shi, Yunyu ^a   Liu, Haiyan ^a  

^a UNIVERSITY OF SCIENCE AND TECHNOLOGY OF CHINA   (China)

Author keywords

[No Author keywords available]

Indexed keywords

COMPUTER SIMULATION; DEGREES OF FREEDOM (MECHANICS); MOLECULAR DYNAMICS; MOLECULAR STRUCTURE; MONTE CARLO METHODS; NUCLEAR MAGNETIC RESONANCE; PHASE TRANSITIONS; POLYPEPTIDES; RELAXATION PROCESSES; SAMPLING;

HELICAL STRUCTURE;

PROTEINS;

EID: 0042378853     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.1591717     Document Type: Article

References (33)

1. S. Doniach and P. Eastman, Curr. Opin. Struct. Biol. 9, 157 (1999).
2. V. Daggett, Curr. Opin. Struct. Biol. 10, 160 (2000).
3. M. A. Balsera, W. Wriggers, Y. Oono, and K. Schulten, J. Phys. Chem. 100, 2567 (1996).
4. L. S. D. Caves, J. D. Evanseck, and M. Karplus, Protein Sci. 7, 649 (1998).
5. P. Eastman, M. Pellegrini, and S. Doniach, J. Chem. Phys. 110, 10141 (1999).
6. N. Nakajima, H. Nakamura, and A. Kidera, J. Phys. Chem. B 101, 817 (1997).
7. F. Yasar, H. Arkin, T. Cclik, B. A. Berg, and H. Meirovitch, J. Comput. Chem. 23, 1127 (2002).
8. C. Bartels and M. Karplus, J. Comput. Chem. 18, 1450 (1997).
9. C. Bartels and M. Karplus, J. Phys. Chem. B 102, 865 (1998).
10. C. Bartels, K. Schulten, and M. Karplus, Theor. Chem. Acc. 101, 62 (1999).
11. H. Grubmuller, Phys. Rev. E 52, 2893 (1995).
12. T. Huber, A. E. Torda, and W. F. van Gunsteren, J. Comput. Aided. Mol. Des. 8, 695 (1994).
13. Y. Pak and S. Wang, J. Chem, Phys. 111, 4359 (1999).
14. A. Amadei, A. B. M. Linssen, and H. J. C. Berendsen, Proteins: Struct., Funct., Genet. 17, 412 (1993).
15. A. Amadei, A. B. M. Linssen, B. L. de Groot, D. M. F. van Aalten, and H. J. C. Berendsen, J. Biomol. Struct, Dyn. 13, 615 (1996).
16. B. L. de Groot, A. Amadei, N. A. J. van Nuland, and H. J. C. Berendsen, Proteins 26, 314 (1996).
17. B. L. de Groot, A. Amadei, D. M. F. van Aalten, and H. J. C. Berendsen, J. Biomol. Struct. Dyn. 13, 741 (1996).
18. B. L. de Groot, S. Hayward, D. M. F. van Aalten, and A. Amadei, Proteins 31, 116 (1998).
19. A. Ghosh, R. Eiber, and H. A. Scheraga, Proc. Natl. Acad. Sci. U.S.A. 99, 10394 (2002).
20. R. Eiber, A. Ghosh, and A. Cardenas, Acc. Chem. Res. 35, 396 (2002).
21. J. Ma, P. B. Sigler, Z. Xu, and M. Karplus, J. Mol. Biol. 302, 303 (2000).
22. C. Tsallis, J. Stat. Phys. 52, 479 (1988).
23. A. R. Atilgan, S. R. Durell, R. L. Ernigan, and M. C. Demirel, Biophys. J. 80, 505 (2001).
24. A. E. Garcia, Phys. Rev. Lett. 68, 2696 (1992).
25. N. Go, Biophys. Chem. 35, 105 (1990).
26. H. J. C. Berendsen, J. P. M. Postma, W. F. van Gunsteren, A. Di Nola, and J. P. Haak, J. Chem. Phys. 81, 3684 (1984).
27. J. Tirado-Rives and W. L. Jorgensen, Biochemistry 30, 3867 (19910).
28. X. Be, Y. Hong, J. Wei, E. J. Androphy, J. J. Chen, and J. D. Baleja, Biochemistry 40, 1293 (2001).
29. S. Honda, N. Kobayashi, E. Munekata, and H. Uedaira, Biochemistry 38, 1203 (1999).
30. J. P. Ryckaert, G. Ciccotti, and H. J. C. Berendsen, J. Comput. Chem. 23, 327 (1977).
31. W. R. P. Scott, P. H. Hünenberger, I. G. Tironi, A. E. Mark, S. R. Billeter, J. Fennen, A. E. Torda, T. Huber, P. Krüger, and W. F. van Gunsteren, J. Phys. Chem. A 103, 3596 (1999).
32. J. Zhu, Y. Shi, and H. Liu, J. Phys. Chem. B 106, 4844 (2002).
33. Y. Duan, L. Wang, and P. A. Kollman, Proc. Natl. Acad. Sci. U.S.A. 95, 9897 (1998).