Growth-based optimization algorithm for lattice heteropolymers

Physical Review E - Statistical, Nonlinear, and Soft Matter Physics

Volumn 68, Issue 2, 2003, Pages 021113/1-021113/4

  Hsu, Hsiao Ping ^a   Mehra, Vishal ^a   Nadler, Walter ^a   Grassberger, Peter ^a  

^a FORSCHUNGSZENTRUM JÜLICH   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 84988745163     PISSN: 1063651X     EISSN: None     Source Type: Journal    
DOI: 10.1103/PhysRevE.68.021113     Document Type: Article

References (34)

1. K.A. Dill, Biochemistry 24, 1501 (1985).
2. K.F. Lau and K.A. Dill, Macromolecules 22, 3986 (1989)
3. H.S. Chan and K. Dill, J. Chem. Phys. 95, 3775 (1991)
4. D. Shortle, H.S. Chan, and K.A. Dill, Protein Sci. 1, 201 (1992).
5. HP models cannot explain calorimetric cooperativity: H.S. Chan, Proteins 40, 543 (2000).
6. K. Yue et al., Proc. Natl. Acad. Sci. U.S.A. 92, 325 (1995).
7. R. Ramakrishnan, B. Ramachandran and J.F. Pekny, J. Chem. Phys. 106, 2418 (1997).
8. J.M. Deutsch, J. Chem. Phys. 106, 8849 (1997).
9. E.M. O'Toole and A.Z. Panagiotopoulos, J. Chem. Phys. 97, 8644 (1992).
10. H. Frauenkron, U. Bastolla, E. Gerstner, P. Grassberger, and W. Nadler, Phys. Rev. Lett. 80, 3149 (1998).
11. U. Bastolla, H. Frauenkron, E. Gerstner, P. Grassberger, and W. Nadler, Proteins 32, 52 (1998).
12. J.L. Zhang and J.S. Liu, J. Chem. Phys. 117, 3492 (2002).
13. T.C. Beutler and K.A. Dill, Protein Sci. 5, 2037 (1996).
14. R. Ungar and J. Moult, J. Mol. Biol. 231, 75 (1993).
15. R. König and T. Dandekar, Protein Eng. 14, 329 (2001).
16. A. Irbáck, in Monte Carlo Approach to Biopolymers and Protein Folding, edited by P. Grassberger et al. (World Scientific, Singapore, 1998), pp. 98-109.
17. G. Chikenji, M. Kikuchi, and Y. Iba, Phys. Rev. Lett. 83, 1886 (1999).
18. G. Chikenji and M. Kikuchi, Proc. Natl. Acad. Sci. U.S.A. 97, 14273 (2000).
19. F. Liang and W.H. Wong, J. Chem. Phys. 115, 3374 (2001).
20. L. Toma and S. Toma, Protein Sci. 5, 147 (1996).
21. K. Yue and K.A. Dill, Phys. Rev. E 48, 2267 (1993)
22. K. Yue and K.A. Dill, Proc. Natl. Acad. Sci. U.S.A. 92, 146 (1995).
23. P. Grassberger, Phys. Rev. E 56, 3682 (1997).
24. M.N. Rosenbluth and A.W. Rosenbluth, J. Chem. Phys. 23, 356 (1955).
25. D. Aldous and U. Vazirani, in Proceedings of the 35th IEEE Symposium on Foundations of Computer Science, edited by (IEEE, New York, 1994). pp. 492-501.
26. H. Kahn, in Use of Different Monte Carlo Sampling Techniques, Symposium on the Monte Carlo Method, edited by H. A. Meyer (Wiley, New York, 1956).
27. J.S. Liu, Monte Carlo Strategies in Scientific Computing, Springer Series in Statistics (Springer, New York, 2001).
28. H.-P. Hsu, V. Mehra, W. Nadler, and P. Grassberger, (unpublished).
29. H. Frauenkron, M.S. Causo, and P. Grassberger, Phys. Rev. E 59, R16 (1999).
30. HP = 0.2 never was detrimental and typically reduced the CPU times by factors between 2 and 10. For the 103-mer from Refs. [18,29,30], we even found a new lowest energy E = 55.
31. R. König and T. Dandekar, BioSystems 50, 17 (1999).
32. K.A. Dill, K. Fiebig, and H.S. Chan, Proc. Natl. Acad. Sci. U.S.A. 90, 1942 (1993).
33. E.E. Lattman, K.M. Fiebig, and K.A. Dill, Biochemistry 33, 6158 (1994).
34. P. Grassberger, e-print cond-mat/0040265.