Repository: Freie Universität Berlin, Math Department

Markov state models and molecular alchemy

Schütte, Ch. and Nielsen, A. and Weber, M. (2015) Markov state models and molecular alchemy. Molecular Physics, 113 (1). pp. 69-78. ISSN 0026-8976

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In recent years, Markov state models (MSMs) have attracted a considerable amount of attention with regard to modelling conformation changes and associated function of biomolecular systems. They have been used successfully, e.g. for peptides including time-resolved spectroscopic experiments, protein function and protein folding , DNA and RNA, and ligand-receptor interaction in drug design and more complicated multivalent scenarios. In this article, a novel reweighting scheme is introduced that allows to construct an MSM for certain molecular system out of an MSM for a similar system. This permits studying how molecular properties on long timescales differ between similar molecular systems without performing full molecular dynamics simulations for each system under consideration. The performance of the reweighting scheme is illustrated for simple test cases, including one where the main wells of the respective energy landscapes are located differently and an alchemical transformation of butane to pentane where the dimension of the state space is changed.

Item Type:Article
Subjects:Mathematical and Computer Sciences
Divisions:Department of Mathematics and Computer Science > Institute of Mathematics > BioComputing Group
ID Code:1468
Deposited By: BioComp Admin
Deposited On:27 Nov 2014 12:08
Last Modified:23 Oct 2015 13:29

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