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Distributions are available as zipped java executables and associated materials, or as a zipped netbeans project with associated libraries (in JARs) and pre-built executables.
MSMExplorer
A Visualization Application for Markov State Models for protein-folding simulations generated by MSMBuilder
MSMExplorer 0.9
Dec 28, 2012

Some bug fixes and a new walkthrough for learning MSMExplorer  View License

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