Monte Carlo simulations of the HP model (the "ising model" of protein folding)

Computer Physics Communications

Volumn 182, Issue 9, 2011, Pages 1896-1899

  Li, Ying Wai ^a   Wüst, Thomas ^b   Landau, David P ^a  

^a UNIVERSITY OF GEORGIA   (United States)

^b SWISS FEDERAL RESEARCH INSTITUTE WSL   (Switzerland)

Author keywords

Adsorption; Heteropolymers; HP model; Protein folding; Wang Landau sampling

Indexed keywords

ATTRACTIVE SURFACES; DENSITY OF STATE; HETEROPOLYMERS; HP MODEL; INTERACTION STRENGTH; MONTE CARLO SIMULATION; MONTE CARLO TRIALS; NATIVE STATE; PROTEIN MODELS; SHORT SEQUENCES; SURFACE ADSORPTION; WANG-LANDAU SAMPLING;

ADSORPTION; COMPUTER SIMULATION; ISING MODEL; PROTEIN FOLDING; PROTEINS;

MONTE CARLO METHODS;

EID: 79958130447     PISSN: 00104655     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cpc.2010.12.049     Document Type: Article

References (21)

1. C. Branden, and J. Tooze Introduction to Protein Structure 1991 Garland New York
2. J.D. Bryngelson, J.N. Onuchic, N.D. Socci, and P.G. Wolynes Protein Struct. Funct. Genet. 21 1995 167
3. K.A. Dill, S.B. Ozkan, M.S. Shell, and T.R. Weikl Annu. Rev. Biophys. Biomol. Struct. 37 2008 289
4. J.R. Banavar, and A. Maritan Annu. Rev. Biophys. Biomol. Struct. 36 2007 261
5. K.A. Dill Biochemistry 24 1985 1501
6. K.F. Lau, and K.A. Dill Macromolecules 22 1989 3986
7. B. Berger, and T. Leighton J. Comput. Biol. 5 1998 27
8. P. Crescenzi J. Comput. Biol. 5 1998 409
9. M. Bachmann, and W. Janke Phys. Rev. E 73 2006 020901(R)
10. N. Lesh, M. Mitzenmacher, S. Whitesides, in: RECOMB, 2003, p. 188.
11. J.M. Deutsch J. Chem. Phys. 106 1997 8849
12. T. Wüst, and D.P. Landau Phys. Rev. Lett. 102 2009 178101
13. F. Wang, and D.P. Landau Phys. Rev. Lett. 86 2001 2050
14. F. Wang, and D.P. Landau Phys. Rev. E 64 2001 056101
15. F. Wang, and D.P. Landau Comput. Phys. Comm. 147 2002 674
16. A.D. Swetnam, and M.P. Allen Phys. Chem. Chem. Phys. 11 2009 2046
17. M. Bachmann, and W. Janke J. Chem. Phys. 120 2004 6779
18. T. Wüst, and D.P. Landau Comput. Phys. Comm. 179 2008 124
19. Y.W. Li, T. Wuest, D.P. Landau, Nanophenomena at Surfaces, in: M. Michailov (Ed.), Springer Series in Surface Sciences, vol. 47, Springer-Verlag, Berlin, Heidelberg, 2011, Chapter 7, doi:10.1007/978-3-642-16510-8-7, in press.
20. T. Vogel, M. Bachmann, and W. Janke Phys. Rev. E 76 2007 061803
21. M. Möddel, W. Janke, and M. Bachmann Phys. Chem. Chem. Phys. 12 2010 11548