Pairwise contact potentials are unsuitable for protein folding

Journal of Chemical Physics

Volumn 109, Issue 24, 1998, Pages 11101-11108

  Vendruscolo, Michele ^a   Domany, Eytan ^a  

^a WEIZMANN INSTITUTE OF SCIENCE   (Israel)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 0000171351     PISSN: 00219606     EISSN: None     Source Type: Journal    
DOI: 10.1063/1.477748     Document Type: Article

References (41)

1. Protein Folding, edited by T. E. Creighton (Freeman, New York, 1992).
2. D. Duboule, Science 278, 555 (1997), and references therein.
3. J. D. Watson et al., Recombinant DNA (Freeman, New York, 1992).
4. H. S. Chan and K. A. Dill, Proc. Natl. Acad. Sci. USA 87, 6388 (1990).
5. A. Godzik, J. Skolnik, and A. Kolinski, Protein Eng. 6, 801 (1993).
6. L. Holm and C. Sander, J. Mol. Biol. 233, 123 (1993).
7. L. Mirny and E. Domany, Proteins 26, 391 (1996).
8. M. Vendruscolo, E. Kussell, and E. Domany, Folding Des. 2, 295 (1997).
9. G. Crippen and T. F. Havel, Distance Geometry and Molecular Conformation (Wiley, New York, 1988).
10. A. T. Brünger, P. D. Adams, and L. M. Rice, Curr. Opin. Struct. Biol. 5, 325 (1997).
11. M. Vendruscolo and E. Domany, Folding Des. 3, 329 (1998).
12. S. Miyazawa and R. L. Jernigan, J. Mol. Biol. 256, 623 (1996).
13. D. A. Hinds and M. Levitt, J. Mol. Biol. 243, 668 (1994).
14. P. D. Thomas and K. A. Dill, J. Mol. Biol. 257, 457 (1996).
15. R. L. Jernigan and I. Bahar, Curr. Opin. Struct. Biol. 6, 195 (1996).
16. J. Skolnick, L. Jaroszewski, A. Kolinski, and A. Godzik, Protein Sci. 6, 676 (1997).
17. C. M.-R. Lemer, M. J. Rooman, and S. J. Wodak, Proteins 23, 337 (1995).
18. M. N. Maiorov and G. M. Crippen, J. Mol. Biol. 227, 876 (1992).
19. R. A. Goldstein, Z. Luthey-Shulten, and P. G. Wolynes, Proc. Natl. Acad. Sci. USA 89, 9029 (1992).
20. M.-H. Hao and A. Scheraga, Proc. Natl. Acad. Sci. USA 93, 4984 (1996).
21. M.-H. Hao and A. Scheraga, J. Phys. Chem. 100, 14540 (1996).
22. L. A. Mirny and E. I. Shakhnovich, J. Mol. Biol. 264, 1164 (1996).
23. J. M. Deutsch and T. Kurosky, Phys. Rev. E 56, 4553 (1997).
24. F. Seno, A. Maritan, and J. R. Banavar, Proteins 30, 244 (1998).
25. F. Rosenblatt, Principles of Neurodynamics (Spartan, New York, 1962).
26. M. L. Minsky and S. A. Papert, Perceptrons (MIT Press, Cambridge, MA, 1969).
27. T. Cover, IEEE Trans. Elect. Comput. 14, 326 (1965).
28. E. Gardner, J. Phys. A 21, 257 (1988).
29. D. Nabutovski and E. Domany, Neural Comput. 3, 604 (1991).
30. M. Vendruscolo, B. Subramanian, I. Kanter, E. Domany, and J. Lebowitz, Phys. Rev. E (in press).
31. The number of self-avoiding walk configurations is also exponential, albeit with a larger coefficient of N in the exponent.
32. D. Fisher, D. Rice, J. U. Bowie, and D. Eisenberg, FASEB J. 10, 126 (1996).
33. A. V. Finkelstein, Curr. Opin. Struct. Biol. 7, 60 (1997).
34. C. Wilson and S. Doniach, Proteins 6, 193 (1989).
35. A. Kolinski and J. Skolnick, Proteins 18, 353 (1994).
36. A. Šali, E. I. Shakhnovich, and M. Karplus, J. Mol. Biol. 235, 1614 (1994).
37. M. N. Teeter, S. M. Roe, and N. H. Heo, J. Mol. Biol. 230, 292 (1993).
38. K. F. Lau and K. A. Dill, Macromolecules 22, 3986 (1989).
39. M.-H. Hao and A. Scheraga, J. Mol. Biol. 277, 973 (1998).
40. J. Van Mourik, C. Clementi, A. Maritan, A. F. Seno, and J. R. Banavar, E-print cond-mat/9801137.
41. E. Domany, L. Mirny, M. Vendruscolo, and E. I. Shakhnovich (unpublished, 1998).