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EMMA - A software package for Markov model building and analysis

Please always quote using this URN:urn:nbn:de:0296-matheon-10545
  • Folding and conformational changes of macromolecules often require the generation of large amounts of simulation data that are difficult to ana- lyze. Markov state models (MSMs) address this challenge by providing a systematic way to decompose the state space of the molecular system into substates and to estimate a transition matrix containing the transi- tion probabilities between these substates. This transition matrix can be analyzed to reveal the metastable, i.e. long-living, states of the system, its slowest relaxation timescales and transition pathways and rates e.g. from unfolded to folded, or from dissociated to bound states. To reduce the technical burden of constructing such MSMs we provide the software framework EMMA (available at https://simtk.org/home/emma) to con- struct, validate and analyse such Markov State Models.

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Metadaten
Author:Martin Senne, Christof Schütte, Frank Noe
URN:urn:nbn:de:0296-matheon-10545
Referee:Christof Schütte
Document Type:Preprint, Research Center Matheon
Language:English
Date of first Publication:2012/02/02
Release Date:2012/02/02
Institute:Research Center Matheon
Freie Universität Berlin
MSC-Classification:60-XX PROBABILITY THEORY AND STOCHASTIC PROCESSES (For additional applications, see 11Kxx, 62-XX, 90-XX, 91-XX, 92-XX, 93-XX, 94-XX) / 60-08 Computational methods (not classified at a more specific level) [See also 65C50]
68-XX COMPUTER SCIENCE (For papers involving machine computations and programs in a specific mathematical area, see Section {04 in that areag 68-00 General reference works (handbooks, dictionaries, bibliographies, etc.) / 68-01 Instructional exposition (textbooks, tutorial papers, etc.)
Preprint Number:915
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