All-atom folding of the trp-cage protein with an adpative parallel tempering method

Europhysics Letters

Volumn 67, Issue 2, 2004, Pages 307-313

  Schug, A ^a   Wenzel, W ^a  

^a KARLSRUHE INSTITUTE OF TECHNOLOGY   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

EID: 3142735955     PISSN: 02955075     EISSN: None     Source Type: Journal    
DOI: 10.1209/epl/i2004-10056-2     Document Type: Article

References (32)

1. BAKER D. and SALI A., Science, 294 (2001) 93.
2. PlLLARDY J., CZAPLEWSKI C., LIWO A., LEE J., RIPOLL D. R., KAMIERKIEWICZ R., OLDZIEJ S., WEDEMEYER W. J., GIBSON K. D., ARNAUTOVA Y. A., SAUNDERS J., YE Y.-J. et al., Proc. Natl. Acad. Sci. USA, 98 (2001) 2329.
3. SCHONBRUNN J., WEDEMEYER W. J. and BAKER D., Curr. Opinion Struct. Biol., 12 (2002) 348.
4. SCHUG A., HERGES T. and WENZEL W., Phys. Rev. Lett., 91 (2003) 158102.
5. HERGES T. and WENZEL W., Reproducible in-silico folding of a three-helix protein in a transferable all-atom forcefield, http://www.arXiv.org:physics/ 0310146 (2004).
6. VILA J., RIPOLL D. and SCHERAGA H., Proc. Natl. Acad. Sci. USA, 100 (2004) 14812.
7. HERGES T. and WENZEL W., Development of an all-atom forcefield for tertiary structure prediction of helical proteins, submitted to Biophys. J. (2004).
8. HANSMANN U. H. E., Phys. Rev. Lett., 88 (2002) 068105.
9. DREWS J., Science, 287 (2000) 1960.
10. MERLITZ H., BURGHARDT B. and WENZEL W., Chem. Phys. Lett., 370 (2003) 68.
11. LATTMAN E., Proteins, 44 (2001) 399.
12. BONNEAU R., TSUI J., RUCZINSKI I., CHIVIAN D., STRAUSS C. M. E. and BAKER D., Proteins, 45 (2001) 119.
13. DUAN Y. and KOLLMAN P. A., Science, 282 (1998) 740.
14. SNOW C. D., NGUYEN H., PANDA V. S. and GRUEBELE M., Nature, 420 (2002) 102.
15. SIMMERLING C., STROCKBINE B. and ROITBERG A., J. Am. Chem. Soc., 124 (2002) 11258.
16. ANFINSEN C. B., Science, 181 (1973) 223.
17. HERGES T., SCHUG A. and WENZEL W., Protein Structure Prediction with Stochastic Optimization Methods: Folding and Misfolding the Villin Headpiece, to be published in Lect. Notes Comput. Sci. (Springer, New York) 2004.
18. HERGES T., SCHUG A. and WENZEL W., All atom folding and misfolding of the villin headpiece in a free-energy forcefield (2004), (submitted).
19. NEIDIGH J. W., FESINMEYER R. M. and ANDERSON N. H., Nature Struct. Biol., 9 (2002) 425.
20. QIU L., PABIT S. A., ROITBERG A. E. and HAGEN S. J., J. Am. Chem. Soc., 124 (2002) 12952.
21. HERGES T., MERLITZ H. and WENZEL W., J. Ass. Lab. Autom., 7 (2002) 98.
22. ABAGYAN R. and TOTROV M., J. Mol. Biol., 235 (1994) 983.
23. HERGES T., SCHUG A., BURGHARDT B. and WENZEL W., Low Energy Conformations of a Three Helix Peptide in an All-Atom Biomolecular Forcefield, to be published in Int. J. Quantum Chem. (2004).
24. AVBELJ F. and MOULT J., Biochemistry, 34 (1995) 755.
25. EISENBERG D. and McLACHLAN A. D., Nature, 319 (1986) 199.
26. SHARP K. A., NICHOLLS A., FRIEDMAN R. and HONIG B., Biochemistry, 30 (1991) 9686.
27. MARINARI E. and PARISI G., Europhys. Lett., 19 (1992) 451.
28. LYUBARTSEV A. P., MARTINOVSKI A. A., SHEVKUNOV S. V. and VORONTSOV-VELYAMINOV P., J. Chem. Phys., 96 (1992) 1776.
29. HANSMANN U. and OKAMOTO Y., J. Comput. Chem., 18 (1997) 920.
30. HANSMANN U., Eur. Phys. J. B, 12 (1999) 607.
31. LIN C., HU C. and HANSMANN U., Proteins, 53 (2003) 436.
32. NAYEEM A., VILA J. and SCHERAGA H., J. Comput. Chem., 12 (1991) 594.