Markov state models and molecular alchemy

Molecular Physics

Volumn 113, Issue 1, 2015, Pages 69-78

  Schütte, Christof ^a,b   Nielsen, Adam ^b   Weber, Marcus ^b  

^a FREIE UNIVERSITÄT BERLIN   (Germany)

^b ZUSE INSTITUTE BERLIN   (Germany)

Author keywords

Markov state models; molecular alchemy; molecular dynamics; reweighting

Indexed keywords

NUCLEIC ACIDS; PROTEINS;

ASSOCIATED FUNCTIONS; BIOMOLECULAR SYSTEM; LIGAND-RECEPTOR INTERACTIONS; MARKOV STATE MODELS; MOLECULAR ALCHEMY; MOLECULAR DYNAMICS SIMULATIONS; MOLECULAR PROPERTIES; RE-WEIGHTING;

MOLECULAR DYNAMICS;

EID: 84918815282     PISSN: 00268976     EISSN: 13623028     Source Type: Journal    
DOI: 10.1080/00268976.2014.944597     Document Type: Article

References (24)

1. M. Praprotnik, L.D. Site, and, K. Kremer., J. Chem. Phys. 123, 224106 (2005).
2. C. Schütte, and, M. Sarich., Metastability and Markov State Models in Molecular Dynamics: Modeling, Analysis, Algorithmic Approaches (AMS, Berlin, 2013).
3. J.-H. Prinz, H. Wu, M. Sarich, B. Keller, M. Senne, M. Held, J.D. Chodera, C. Schütte, and, F. Noé., J. Chem. Phys. 134, 174105 (2011).
4. N.V. Buchete, and, G. Hummer., J. Phys. Chem. B 112, 6057 (2008).
5. J.-, H. Prinz, B. Keller, and, F. Noé., Phys. Chem. Chem. Phys. 13 (38), 16912-16927 (2011).
6. B. Keller, A.Y. Kobitski, U.G. Nienhaus, and, F. Noé., J. Am. Chem. Soc. 136, 4534 (2014).
7. J.D. Chodera, K.A. Dill, N. Singhal, V.S. Pande, W.C. Swope, and, J.W. Pitera., J. Chem. Phys. 126, 155101 (2007).
8. F. Noé, C. Schütte, E. Vanden-Eijnden, L. Reich, and, T.R. Weikl., Proc. Natl. Acad. Sci. U.S.A. 106, 19011 (2009).
9. G.R. Bowman, K.A. Beauchamp, G. Boxer, and, V.S. Pande., J. Chem. Phys. 131 (12), 124101 (2009).
10. I. Horenko, E. Dittmer, F. Lankas, J. Maddocks, Ph. Metzner, and, C. Schütte., SIAM J. Appl. Dyn. Syst. 7 (2), 532-560 (2009).
11. P. Deuflhard, and, C. Schütte., in Applied Mathematics Entering the 21st Century, edited by J.M. Hill and R. Moore. (SIAM, Sydney, 2004), pp. 91-119.
12. A. Bujotzek, and, M. Weber., J. Bioinform. Comput. Biol. 7 (5), 811-831 (2009).
13. M. Weber, A. Bujotzek, and, R. Haag., J. Chem. Phys. 137 (5), 054111 (2012).
14. M. Shan, K.E. Carlson, A. Bujotzek, A. Wellner, R. Gust, M. Weber, J.A. Katzenellenbogen, and, R. Haag., ACS Chem. Biol. 8 (4), 707-715 (2013).
15. A. Mitchell., Nat. Rev. Mol. Cell Biol. 1, 164 (2000).
16. J. Skilling., Bayesian Analysis 1, 833 (2006).
17. G.M. Torrie, and J.-, P. Valleau., J. Comput. Phys. 23, 187 (1977).
18. A.M. Ferrenberg, and, R.H. Swendsen., Phys. Rev. Lett. 63, 1195 (1989).
19. R.H. Swendsen, and, J.S. Wang., Phys. Rev. Lett. 57, 2607 (1986).
20. J.-H. Prinz, J.D. Chodera, V.S. Pande, W.C. Swope, J.C. Smith, and, F. Noé., J. Chem. Phys. 134, 244108 (2011).
21. J.D. Chodera, W.C. Swope, F. Noé, J.-H. Prinz, and, V.S. Pande., J. Chem. Phys. 134, 244107 (2011).
22. B.K. Øksendal., Stochastic Differential Equations: An Introduction with Applications, 6th ed. (Springer-Verlag, Berlin, Heidelberg, New York, 2003).
23. D.W. Stroock, and, S.R.S. Varadhan., Multidimensional Diffusion Processes (Springer, Berlin, Heidelberg, 2006).
24. H. Wang, C. Hartmann, and, C. Schütte., Mol. Phys. 111 (22-23), 3555-3564 (2013).