Using generalized ensemble simulations and Markov state models to identify conformational states

Methods

Volumn 49, Issue 2, 2009, Pages 197-201

  Bowman, Gregory R ^a   Huang, Xuhui ^b   Pande, Vijay S ^a  

^a STANFORD UNIVERSITY   (United States)

^b Stanford University   (United States)

Author keywords

Clustering; Kinetics; Molecular dynamics; Thermodynamics

Indexed keywords

RNA;

ALGORITHM; ARTICLE; COMPUTER SIMULATION; CONFORMATION; KINETICS; MOLECULAR DYNAMICS; PRIORITY JOURNAL; TEMPERATURE; THERMODYNAMICS;

ALGORITHMS; BIOPHYSICS; CLUSTER ANALYSIS; COMPUTER SIMULATION; KINETICS; MARKOV CHAINS; NUCLEIC ACID CONFORMATION; PROGRAMMING LANGUAGES; RNA; SOFTWARE; THERMODYNAMICS;

EID: 63449118443     PISSN: 10462023     EISSN: 10959130     Source Type: Journal    
DOI: 10.1016/j.ymeth.2009.04.013     Document Type: Article

References (30)

1. Mitsutake A., Sugita Y., and Okamoto Y. Biopolymers 60 (2001) 96-123
2. Hansmann U.H., and Okamoto Y. Curr. Opin. Struct. Biol. 9 (1999) 177-183
3. Sugita Y., and Okamoto Y. Chem. Phys. Lett. 314 (1999) 141-151
4. Lyubartsev A.P., Martsinovski A.A., Shevkunov S.V., and Vorontsov-Velyaminov P.N. J. Chem. Phys. 96 (1992) 1776-1783
5. Marinari E., and Parisi G. Eur. Lett. 19 (1992) 451-458
6. Zhou R., Berne B.J., and Germain R. Proc. Natl. Acad. Sci. USA 98 (2001) 14931-14936
7. Rhee Y.M., and Pande V.S. Biophys. J. 84 (2003) 775-786
8. Nymeyer H., and Garcia A.E. Proc. Natl. Acad. Sci. USA 100 (2003) 13934-13939
9. Zhou R. Proc. Natl. Acad. Sci. USA 100 (2003) 13280-13285
10. Krivov S.V., and Karplus M. Proc. Natl. Acad. Sci. USA 101 (2004) 14766-14770
11. Noe F., and Fischer S. Curr. Opin. Struct. Biol. 18 (2008) 154-162
12. Karpen M.E., Tobias D.J., and Brooks III C.L. Biochemistry 32 (1993) 412-420
13. Shao J.Y., Tanner S.W., Thompson N., and Cheatham T.E. J. Chem. Theory Comput. 3 (2007) 2312-2334
14. C. Schutte, Conformational Dynamics: Modeling, Theory, Algorithm, and Application to Biomolecules. Habilitation Thesis, Department of Mathematics and Computer Science, Freie Universitat, Berlin, 1999, pp. 1-139.
15. Chodera J.D., Singhal N., Pande V.S., Dill K.A., and Swope W.C. J. Chem. Phys. 126 (2007) 155101
16. Buchete N.V., and Hummer G. J. Phys. Chem. B 112 (2008) 6057-6069
17. Swope W.C., Pitera J.W., and Suits F. J. Phys. Chem. B 108 (2004) 6571-6581
18. Sriraman S., Kevrekidis L.G., and Hummer G. J. Phys. Chem. B 109 (2005) 6479-6484
19. Frauenfelder H., Sligar S.G., and Wolynes P.G. Science 254 (1991) 1598-1603
20. Yang W.Y., and Gruebele M. J. Am. Chem. Soc. 126 (2004) 7758-7759
21. Singhal N., Snow C., and Pande V.S. J. Chem. Phys. 121 (2004) 415-425
22. Elmer S., Park S., and Pande V.S. J. Chem. Phys. 122 (2005) 124908
23. Jayachandran G., Vishal V., and Pande V.S. J. Chem. Phys. 124 (2006) 164902
24. Kelley N.W., Vishal V., Jaykumar R., Liu C., Pray T., Krafft G., and Pande V.S. J. Chem. Phys. 129 (2008) 214707
25. Gonzalez T. Theor. Comput. Sci. 38 (1985) 293-306
26. Dasgupta S., and Long P.M. J. Comput. Syst. Sci. 70 (2005) 555-569
27. Lindahl E., Hess B., and van der Spoel D. J. Mol. Model. 7 (2001) 306-317
28. Deuflhard P., and Weber M. Linear Algebra Appl. 398 (2005) 161-184
29. Deuflhard P., Huisinga W., Fischer A., and Schütte C. Linear Algebra Appl. 315 (2000) 39-59
30. Hinrichs N.S., and Pande V.S. J. Chem. Phys. 126 (2007) 244101