A comparison of generalized Born methods in folding simulations

Chemical Physics Letters

Volumn 460, Issue 1-3, 2008, Pages 295-299

  Terada, Tohru ^a   Shimizu, Kentaro ^a  

^a UNIVERSITY OF TOKYO   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

DIELECTRIC DEVICES; DYNAMICS; FREE ENERGY; MOLECULAR DYNAMICS; QUANTUM CHEMISTRY;

AVERAGE ERRORS; CHIGNOLIN; ELSEVIER (CO); FREE-ENERGY LANDSCAPES; GENERALIZED BORN; MULTICANONICAL MOLECULAR DYNAMICS (MCMD); NATIVE STRUCTURES;

PROTEIN FOLDING;

EID: 46849115628     PISSN: 00092614     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.cplett.2008.05.066     Document Type: Article

References (25)

1. Still W.C., Tempczyk A., Hawley R.C., and Hendrickson T. J. Am. Chem. Soc. 112 (1990) 6127
2. Tsui V., and Case D.A. Biopolym. (Nucl. Acid Sci.) 56 (2001) 275
3. Onufriev A., Case D.A., and Bashford D. J. Comput. Chem. 23 (2002) 1297
4. Case D.A., et al. AMBER 6 (1999), University of California, San Francisco
5. Hawkins G.D., Cramer C.J., and Truhlar D.G. Chem. Phys. Lett. 246 (1995) 122
6. Onufriev A., Bashford D., and Case D.A. Proteins 55 (2004) 383
7. Mongan J., Simmerling C., McCammon J.A., Case D.A., and Onufriev A. J. Chem. Theor. Comput. 3 (2007) 156
8. Lee B., and Richards F.M. J. Mol. Biol. 55 (1971) 379
9. Satoh D., Shimizu K., Nakamura S., and Terada T. FEBS Lett. 580 (2006) 3422
10. Simmerling C., Strockbine B., and Roitberg A.E. J. Am. Chem. Soc. 124 (2002) 11258
11. Lei H., Wu C., Liu H., and Duan Y. Proc. Natl. Acad. Sci. USA 104 (2007) 4925
12. Hansmann U.H.E., Okamoto Y., and Eisenmenger F. Chem. Phys. Lett. 259 (1996) 321
13. Mitsutake A., Sugita Y., and Okamoto Y. Biopolym. (Pept. Sci.) 60 (2001) 96
14. Nakajima N., Nakamura H., and Kidera A. J. Phys. Chem. B 101 (1997) 817
15. Honda S., Yamasaki K., Sawada Y., and Morii H. Structure 12 (2004) 1507
16. Terada T., and Kidera A. J. Chem. Phys. 118 (2002) 33
17. Terada T., Matsuo Y., and Kidera A. J. Chem. Phys. 118 (2003) 4306
18. Ferrenberg A.M., and Swendsen R.H. Phys. Rev. Lett. 61 (1988) 2635
19. Späth H. Cluster Analysis Algorithms for Data Reduction and Classification of Objects (1980), Ellis Horwood Limited, England
20. Jorgensen W.L., Chandrasekhar J., Madura J.D., Impey R.W., and Klein M.L. J. Chem. Phys. 79 (1983) 926
21. Berendsen H.J.C., Postma J.P.M., van Gunsteren W.F., DiNola A., and Haak J.R. J. Chem. Phys. 81 (1984) 3684
22. Ryckaert J.-P., Ciccotti G., and Berendsen H.J.C. J. Comput. Phys. 23 (1977) 327
23. Darden T., York D., and Pedersen L. J. Chem. Phys. 98 (1993) 10089
24. Case D.A., et al. AMBER 9 (2006), University of California, San Francisco
25. Kraulis P.J. J. Appl. Cryst. 24 (1991) 946