Exploring the space of protein folding Hamiltonians: The balance of forces in a minimalist β-barrel model

Journal of Chemical Physics

Volumn 109, Issue 7, 1998, Pages 2895-2903

  Shea, Joan Emma ^a   Nochomovitz, Yigal D ^a   Guo, Zhuyan ^a   Brooks, Charles L ^a  

^a SCRIPPS RESEARCH INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0000870658     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.476842     Document Type: Article

References (30)

1. M. Karplus and A. Sali, Curr. Opin. Struct. Biol. 5, 58 (1995).
2. P. S. Kim and R. L. Baldwin, Annu. Rev. Biochem. 59, 631 (1990).
3. M. Karplus and D. L. Weaver, Biopolymers 18, 1421 (1979).
4. J. N. Onuchic, P. G. Wolynes, Z. Luthey-Schulten, and N. D. Socci, Proc. Natl. Acad. Sci. USA 92, 3626 (1995).
5. J. N. Onuchic, N. D. Socci, Z. Luthey-Schulten, and P. G. Wolynes, Folding Design 1, 441 (1996).
6. J. D. Bryngelson, J. N. Onuchic, N. D. Socci, and P. G. Wolynes, Proteins: Struct., Funct., Genet. 21, 167 (1995).
7. E. M. Boczko and C. L. Brooks III, Science 21, 393 (1995).
8. Z. Guo and C. L. Brooks III, Proc. Natl. Acad. Sci. USA 94, 10161 (1997).
9. F. Sheinerman and C. L. Brooks III, Proc. Natl. Acad. Sci. USA 95, 1562 (1998).
10. A. Kolinski and J. Skolnick, Proteins: Struct., Funct., Genet. 18, 338 (1994).
11. E. I. Shakhnovich, G. M. Farztdinov, A. M. Gutin, and M. Karplus, Phys. Rev. Lett. 67, 1665 (1991).
12. E. I. Shakhnovich, Phys. Rev. Lett. 72, 3907 (1994).
13. K. A. Dill, S. Bromberg, K. Yue, K. M. Fiebig, D. P. Yee, P. D. Thomas, and H. S. Chan, Protein Sci. 4, 561 (1995).
14. A. Rey and J. Skolnick, J. Chem. Phys. 158, 1991 (1991).
15. D. Thirumalai and Z. Guo, Biopolymers 35, 137 (1995).
16. J. D. Honeycutt and D. Thirumalai, Proc. Natl. Acad. Sci. USA 87, 3526 (1990).
17. Z. Guo and C. L. Brooks III, Biopolymers 42, 745 (1997).
18. H. Nymeyer, A. E. García, and J. N. Onuchic, Proc. Natl. Acad. Sci. USA (in press).
19. Y. Zhou and M. Karplus, Proc. Natl. Acad. Sci. USA 94, 14429 (1997).
20. A. M. Ferrenberg and R. H. Swensen, Phys. Rev. Lett. 63, 1195 (1989).
21. Z. Guo and D. Thirumalai, Biopolymers 36, 83 (1995).
22. J. N. Honeycutt and D. Thirumalai, Biopolymers 32, 695 (1992).
23. H. C. Anderson, J. Comput. Phys. 52, (1983).
24. S. K. Kumar, D. Bouzida, R. H. Swendsen, P. A. Kollman, and J. M. Rosenberg, J. Comp. Chem. 13, 1011 (1992).
25. A. Kolinski, J. Skolnick, and R. Yaris, J. Chem. Phys. 85, 3585 (1986).
26. T. Veitshans, D. Klimov, and D. Thirumalai, Folding Design 2, 1 (1996).
27. Z. Guo, D. Thirumalai, and J. D. Honeycutt, J. Chem. Phys. 97, 525 (1992).
28. H. S. Chan and K. A. Dill, J. Chem. Phys. 100, 9238 (1994).
29. R. A. Goldstein, Z. A. Luthey-Schulten, and P. G. Wolynes, Proc. Natl. Acad. Sci. USA 89, 9029 (1992).
30. E. I. Shakhnovich and A. M. Gutin, Proc. Natl. Acad. Sci. USA 90, 7195 (1993).