Optimized folding simulations of protein A

European Physical Journal E

Volumn 24, Issue 3, 2007, Pages 311-316

  Trebst, S ^a   Hansmann, U H E ^b,c  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b MICHIGAN TECHNOLOGICAL UNIVERSITY   (United States)

^c FORSCHUNGSZENTRUM JÜLICH   (Germany)

Author keywords

87.14.Ee Proteins; 87.15.Aa Theory and modeling; computer simulation; 87.15.Cc Folding and sequence analysis; 87.15.He Dynamics and conformational changes

Indexed keywords

CONFORMATIONAL CHANGES; ENERGY FUNCTIONS; SEQUENCE ANALYSIS;

COMPUTER SIMULATION; CONFORMATIONS; OPTIMIZATION;

PROTEIN FOLDING;

STAPHYLOCOCCUS PROTEIN A;

ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; PROTEIN DATABASE; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; ROTATION; TEMPERATURE; THERMODYNAMICS;

COMPUTER SIMULATION; DATABASES, PROTEIN; MODELS, MOLECULAR; PROTEIN FOLDING; PROTEIN STRUCTURE, SECONDARY; ROTATION; STAPHYLOCOCCAL PROTEIN A; TEMPERATURE; THERMODYNAMICS;

EID: 37449026144     PISSN: 12928941     EISSN: 1292895X     Source Type: Journal    
DOI: 10.1140/epje/i2007-10241-1     Document Type: Article

References (29)

1. C.J. Geyer, A. Thompson, J. Am. Stat. Assoc. 90, 909 (1995).
2. K. Hukushima, K. Nemoto, J. Phys. Soc. Jpn. 65, 1604 (1996).
3. U.H.E. Hansmann, Y. Okamoto, Phys. Rev. E 56, 2228 (1997).
4. P.M.C. Oliveira, T.J.P. Penna, H.J. Herrmann, Eur. Phys. J. B 1, 205 (1998).
5. S. Kmiecik, A. Kolinski, Proc. Natl. Acad. Sci. U.S.A. 104, 12330 (2007).
6. K. Hamacher, Europhys. Lett. 74, 944 (2006).
7. H. Li, M. Fajer, W. Yang, J. Chem. Phys. 126, 24106 (2007).
8. S. Trebst, D.A. Huse, M. Troyer, Phys. Rev. E 70, 046701 (2004).
9. H.G. Katzgraber, S. Trebst, D.A. Huse, M. Troyer, J. Stat. Mech. P03018 (2006).
10. S. Trebst, M. Troyer, U.H.E. Hansmann, J. Chem. Phys. 124, 174903 (2006).
11. D. Gront, A. Kolinski, J. Phys.: Condens. Matter 19, 036225 (2007).
12. M.J. Sippl, G. Némethy, H.A. Scheraga, J. Phys. Chem. 88, 6231 (1984) and references therein.
13. T. Ooi, M. Obatake, G. Nemethy, H.A. Scheraga, Proc. Natl. Acad. Sci. U.S.A. 84, 3086 (1987).
14. C.-Y. Lin, C-K. Hu, U.H.E. Hansmann, Proteins 52, 436 (2003).
15. H. Gouda, H. Torigoe, A. Saito, M. Sato, Y. Arata, I. Shimada, Biochemistry 31, 9665 (1992).
16. E.M. Boczko, C.L. Brooks III, Science 269, 393 (1995).
17. A. Ghosh, R. Elber, H. Scheraga, Proc. Natl. Acad. Sci. U.S.A. 99, 10394 (2002).
18. G. Favrin, A. Irbäck, S. Wallin, Proteins: Struct. Funct. Genet. 47, 99 (2002).
19. A. Garcia, J.N. Onuchic, Proc. Natl. Acad. Sci. U.S.A. 100, 13898 (2003).
20. T. Herges, W. Wenzel, Biophys. J. 87, 3100 (2004).
21. M. Khalili, A. Liwo, H. Scheraga, J. Mol. Biol. 355, 536 (2006).
22. J.S. Yang, W.W. Chen, J. Skolnick, E.I. Shakhnovich, Structure 15, 53 (2007).
23. R. Zhou, B.J. Berne, Proc. Natl. Acad. Sci. U.S.A. 99, 12777 (2002).
24. N. Nymeyer, A.E. Garcia, Proc. Natl. Acad. Sci. U.S.A. 100, 13934 (2003).
25. F. Eisenmenger, U.H.E. Hansmann, Sh. Hayryan, C.-K. Hu, Comput. Phys. Commun. 138, 192 (2001).
26. F. Eisenmenger, U.H.E. Hansmann, Sh. Hayryan, C.-K. Hu, Comput. Phys. Commun. 174, 422 (2006).
27. U.H.E. Hansmann, Chem. Phys. Lett. 281, 140 (1996).
28. W. Kwak, U.H.E. Hansmann, Phys. Rev. Lett. 95, 138102 (2005).
29. R.A. Abagyan, M. Trotov, J. Comput. Phys. 151, 405 (1999).