Software
software
software
MSMBuilder
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Lane, Thomas
McGibbon, Robert
Bowman, Greg
Beauchamp, Kyle
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University of California, Berkeley
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Open source software license
MSMBuilder is an open source software package for automating the construction and analysis of Markov state models (MSMs). It is primarily written in the python programming language with C extensions for the most time consuming routines. MSMs are a powerful means of modeling the structure and dynamics of molecular systems, like proteins. An MSM is essentially a map of the conformational space a molecule explores. Such models consist of a set of states and a matrix of transition probabilities (or, equivalently, transition rates) between each pair of states. Intuitively, the states in an MSM can be thought of as corresponding to local minima in the free energy landscape that ultimately determines a molecules structure and dynamics. MSMBuilder includes tools for - Constructing an MSM from a set of computer simulations (typically molecular dynamics simulations in standard formats like xtc, dcd, and pdb) - Validating statistical properties of MSMs - Mimicking various experimental protocols to allow a quantitative comparison with experiments - Driving efficient simulations via adaptive sampling (which decides where new simulations should be run to minimize statistical uncertainty in a model) The source code is available under the Downloads link to the left. Installation should take no more than 30 minutes. The video embedded below provides a more thorough introduction to the motivation for and use of MSMBuilder.
Keywords: Free energy landscape, Markov state model
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Linux
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Mac OS X
2012-10-10T08:20:37.276-05:00
nvasilevsky (Nicole Vasilevsky)
2012-10-10T13:19:59.505-05:00
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Published
nvasilevsky (Nicole Vasilevsky)
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