A tutorial on building markov state models with msmbuilder and coarse-graining them with BACE

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Abstract

Markov state models (MSMs) are a powerful means of (1) making sense of molecular simulations, (2) making a quantitative connection between simulation and experiment, and (3) driving efficient simulations. A Markov model can be thought of as a map of the conformational space a molecule explores. Instead of having towns and cities connected with roads labeled with speed limits, a Markov model has conformational states and probabilities of transitioning between pairs of these states. This tutorial describes how to build Markov models and a few of the basic analyses that can be performed with the MSMBuilder software package.

Original languageEnglish
Title of host publicationProtein Dynamics
Subtitle of host publicationMethods and Protocols
PublisherHumana Press Inc.
Pages141-158
Number of pages18
ISBN (Print)9781627036573
DOIs
StatePublished - 2014

Publication series

NameMethods in Molecular Biology
Volume1084
ISSN (Print)1064-3745

Keywords

  • Master equation
  • Molecular dynamics
  • Protein dynamics

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