Non-Markov state model of peptide dynamics

Journal of Molecular Liquids

Volumn 176, Issue , 2012, Pages 65-70

  Nerukh, Dmitry ^a  

^a ASTON UNIVERSITY   (United Kingdom)

Author keywords

Conformational transitions; Markov state model; Non Markov; Protein dynamics

Indexed keywords

CLASSICAL MOLECULAR DYNAMICS; CONFORMATIONAL STATE; CONFORMATIONAL TRANSITIONS; EXPLICIT WATER; MARKOV STATE MODELS; NON-MARKOV; PEPTIDE DYNAMICS; PROTEIN DYNAMICS; STATE MODELS; TIME RESOLUTION;

CONFORMATIONS; MOLECULAR DYNAMICS; PEPTIDES; POLYPEPTIDES;

COMPUTER SIMULATION;

EID: 84870494758     PISSN: 01677322     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molliq.2012.06.011     Document Type: Conference Paper

References (23)

1. C. Schuette, A. Fischer, W. Huisinga, and P. Deuflhard Journal of Computational Physics 151 1 1999 146 168 10.1006/jcph.1999.6231
2. W.C. Swope, J.W. Pitera, and F. Suits The Journal of Physical Chemistry. B 108 21 2004 6571 6581 10.1021/jp037421y arXiv:http://pubs.acs.org/doi/pdf/10. 1021/jp037421y, URL http://pubs.acs.org/doi/abs/10.1021/jp037421y
3. W.C. Swope, J.W. Pitera, F. Suits, M. Pitman, M. Eleftheriou, B.G. Fitch, R.S. Germain, A. Rayshubski, T.J.C. Ward, Y. Zhestkov, and R. Zhou The Journal of Physical Chemistry. B 108 21 2004 6582 6594 10.1021/jp037422q (arXiv:http://pubs.acs.org/doi/pdf/10.1021/jp037422q, URL http://pubs.acs.org/ doi/abs/10.1021/jp037422q)
4. F. Noe, I. Horenko, C. Schuette, and J.C. Smith The Journal of Chemical Physics 126 15 2007 155102 10.1063/1.2714539 (URL http://link.aip.org/link/?JCP/ 126/155102/1)
5. J.D. Chodera, N. Singhal, V.S. Pande, K.A. Dill, and W.C. Swope The Journal of Chemical Physics 126 15 2007 155101 10.1063/1.2714538 (URL http://link.aip.org/link/?JCP/126/155101/1)
6. S. Park, and V.S. Pande The Journal of Chemical Physics 124 5 2006 054118 10.1063/1.2166393 (URL http://link.aip.org/link/?JCP/124/054118/1)
7. J.D. Chodera, W.C. Swope, J.W. Pitera, and K.A. Dill Multiscale Modeling and Simulation 5 4 2006 1214 1226 10.1137/06065146X (URL http://link.aip.org/ link/?MMS/5/1214/1)
8. J.-H. Prinz, H. Wu, M. Sarich, B. Keller, M. Senne, M. Held, J.D. Chodera, C. Schutte, and F. Noe The Journal of Chemical Physics 134 17 2011 174105 10.1063/1.3565032 (URL http://link.aip.org/link/?JCP/134/174105/1)
9. J.P. Crutchfield, and K. Young Physical Review Letters 63 2 1989 105 108
10. J.P. Crutchfield, and K. Young W. Zurek, Entropy, Complexity, and Physics of Information, SFI Studies in the Sciences of Complexity VIII 1990 Addison-Wesley Reading, Massachusetts
11. J.P. Crutchfield Physica D 75 1-3 1994 11 54
12. V. Ryabov, and D. Nerukh Chaos: An Interdisciplinary Journal of Nonlinear Science 21 3 2011 037113 10.1063/1.3608125 (URL http://link.aip.org/link/?CHA/ 21/037113/1)
13. D. Nerukh, C.H. Jensen, and R.C. Glen The Journal of Chemical Physics 132 8 2010 084104 10.1063/1.3328781 (URL http://link.aip.org/link/?JCP/132/084104/ 1)
14. D. Nerukh, V. Ryabov, and M. Taiji Physica A: Statistical Mechanics and its Applications 388 22 2009 4719 4726 10.1016/j.physa.2009.07.041 (URL http://www.sciencedirect.com/science/article/B6TVG-4WXPXVC-1/2/ 02ea8773db9afced932b98cdbfc6cb70)
15. D. van der Spoel, E. Lindahl, B. Hess, G. Groenhof, A.E. Mark, and H.J.C. Berendsen Journal of Computational Chemistry 26 2005 1701 1718
16. B. Hess, and N.F.A. van der Vegt The Journal of Physical Chemistry. B 110 35 2006 17616 17626
17. C. Oostenbrink, T.A. Soares, N.F.A. van der Vegt, and W.F. van Gunsteren European Biophysics Journal with Biophysics Letters 34 4 2005 273 284
18. C. Oostenbrink, A. Villa, A.E. Mark, and W.F. Van Gunsteren Journal of Computational Chemistry 25 13 2004 1656 1676
19. H.J.C. Berendsen, J.P.M. Postma, W.F. van Gunsteren, A. DiNola, and J.R. Haak The Journal of Chemical Physics 81 8 1984 3684 3690
20. C.R. Shalizi, and K.L. Shalizi M. Chickering, J. Halpern, Uncertainty in Artificial Intelligence: Proceedings of the Twentieth Conference 2004 AUAI Press Arlington, Virginia 504 511 URL http://arxiv.org/abs/cs.LG/0406011
21. D.P. Varn, G.S. Canright, and J.P. Crutchfield Physical Review B 66 2002 174110 10.1103/PhysRevB.66.174110 (URL http://link.aps.org/doi/10.1103/PhysRevB. 66.174110)
22. D.P. Varn, G.S. Canright, and J.P. Crutchfield Acta Crystallographica. Section B 63 2 2007 169 182 10.1107/S0108768106043084 (URL http://dx.doi.org/10. 1107/S0108768106043084)
23. C. Shalizi, K. Shalizi, and R. Haslinger Physical Review Letters 93 11 2004 118701-1 118701-4