Everything you wanted to know about Markov State Models but were afraid to ask

Methods

Volumn 52, Issue 1, 2010, Pages 99-105

  Pande, Vijay S ^a   Beauchamp, Kyle ^a   Bowman, Gregory R ^a  

^a STANFORD UNIVERSITY   (United States)

Author keywords

Computer simulation; Distributed computing; Markov State Models; Molecular dynamics; Protein folding

Indexed keywords

COMPUTER SIMULATION; CONFORMATIONAL TRANSITION; DECOMPOSITION; MARKOV STATE MODEL; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN FOLDING; QUANTITATIVE ANALYSIS; REVIEW; THERMODYNAMICS;

COMPUTER SIMULATION; MARKOV CHAINS; PROTEIN FOLDING;

EID: 77956220940     PISSN: 10462023     EISSN: 10959130     Source Type: Journal    
DOI: 10.1016/j.ymeth.2010.06.002     Document Type: Review

References (48)

1. Dill K.A., et al. Annu. Rev. Biophys. 2008, 37:289-316.
2. Snow C.D., et al. Annu. Rev. Biophys. Biomol. Struct. 2005, 34:43-69.
3. Kasson P.M., et al. Proc. Natl. Acad. Sci. USA 2006, 103(32):11916-11921.
4. Kelley N.W., et al. J. Mol. Biol. 2009, 388(5):919-927.
5. Kelley N.W., et al. J. Chem. Phys. 2008, 129(21):214707.
6. Bowman G.R., Huang X., Pande V.S. Methods 2009, 49(2):197-201.
7. Noe F., Fischer S. Curr. Opin. Struct. Biol. 2008, 18(2):154-162.
8. Bowman G.R., et al. J. Chem. Phys. 2009, 131(12):124101.
9. Ensign D.L., Kasson P.M., Pande V.S. J. Mol. Biol. 2007, 374(3):806-816.
10. Gnanakaran S., et al. Curr. Opin. Struct. Biol. 2003, 13(2):168-174.
11. Mitsutake A., Okamoto Y. J. Chem. Phys. 2004, 121(6):2491-2504.
12. Mitsutake A., Sugita Y., Okamoto Y. Biopolymers 2001, 60(2):96-123.
13. Okamoto Y. J. Mol. Graph. Model. 2004, 22(5):425-439.
14. Buchete N.V., Hummer G. Phys. Rev. E Stat. Nonlin. Soft Matter Phys. 2008, 77(Pt. 1):030902.
15. Huang X., et al. Proc. Natl. Acad. Sci. USA 2009, 106(47):19765-19769.
16. Huang X., Bowman G.R., Bacallado S., Pande V.S. Proc. Natl. Acad. Sci. USA 2009, 106:19765-19769.
17. Karpen M.E., Tobias D.J., Brooks C.L. Biochemistry 1993, 32(2):412-420.
18. Shao J., et al. J. Chem. Theory Comput. 2007, 3(6):2312-2334.
19. Noe F., et al. Proc. Natl. Acad. Sci. USA 2009, 106(45):19011-19016.
20. M. Sarich, F. Noe, C. Schutte, SIAM Multiscale Model Simul, in press. Available from: http://publications.mi.fu-berlin.de/771/1/MSM_submitted.pdf.
21. Voelz V.A., et al. J. Am. Chem. Soc. 2010, 132(5):1526-1528.
22. Singhal N., Pande V.S. J. Chem. Phys. 2005, 123(20):204909.
23. Bacallado S., Chodera J.D., Pande V. J. Chem. Phys. 2009, 131(4):045106.
24. Noe F. J. Chem. Phys. 2008, 128(24):244103.
25. Schütte C., et al. J. Comput. Phys. 1999, 151:146-168.
26. Deuflhard P., et al. Lin. Alg. Appl. 2000, 315:39-59.
27. Deuflhard P., Weber M. Lin. Alg. Appl. 2005, 398:161-184.
28. Singhal N., Pande V.S. J. Chem. Phys. 2007, 127:244101.
29. S. Röblitz, Statistical Error Estimation and Grid-free Hierarchical Refinement in Conformation Dynamics, in: Fachbereich Mathematik und Informatik, Freien Universit, Berlin, 2008.
30. Bowman G., Pande V.S. J. Am. Chem. Soc. 2010, 6:787-794.
31. Swope W.C., Pitera J.W., Suits F. J. Phys. Chem. B 2004, 108(21):6571-6581.
32. Park S., Pande V.S. J. Chem. Phys. 2006, 124(5):054118.
33. Metzner P., Schutte C., Vanden-Eijnden E. J. Chem. Phys. 2006, 125(8):084110.
34. Berezhkovskii A., Hummer G., Szabo A. J. Chem. Phys. 2009, 130(20):205102.
35. Noe F., et al. J. Chem. Phys. 2007, 126(15):155102.
36. Sriraman S., Kevrekidis I.G., Hummer G. J. Phys. Chem. B 2005, 109(14):6479-6484.
37. Pan A.C., Roux B. J. Chem. Phys. 2008, 129(6):064107.
38. Sezer D., Freed J.H., Roux B. J. Phys. Chem. B 2008, 112(35):11014-11027.
39. Yang S., Roux B. PLoS Comput. Biol. 2008, 4(3):e1000047.
40. Yang W.Y., et al. J. Mol. Biol. 2004, 336(1):241-251.
41. Elmer S.P., Park S., Pande V.S. J. Chem. Phys. 2005, 123(11):114903.
42. Elmer S.P., Park S., Pande V.S. J. Chem. Phys. 2005, 123(11):114902.
43. Jayachandran G., Vishal V., Pande V.S. J. Chem. Phys. 2006, 124(16):164902.
44. Singhal N., Snow C.D., Pande V.S. J. Chem. Phys. 2004, 121(1):415-425.
45. Chodera J.D., et al. J. Chem. Phys. 2007, 126(15):155101.
46. Kubelka J., Eaton W.A., Hofrichter J. J. Mol. Biol. 2003, 329(4):625-630.
47. Jager M., et al. J. Mol. Biol. 2001, 311(2):373-393.
48. Friedrichs M.S., et al. J. Comput. Chem. 2009, 30(6):864-872.