MSMBuilder pipeline

MSMBuilder specifications


Unique identifier OMICS_13407
Name MSMBuilder
Alternative name Markov State Models Builder
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages C, Python
License GNU Lesser General Public License version 2.1
Computer skills Advanced
Version 3.6.0
Stability Stable
Requirements Numpydoc, matplotlib, iPython-notebook, jinja2, openmm, nbconvert, msmb_data, pyparsing, msmexplorer
Maintained Yes



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  • person_outline Vijay S. Pande <>

Publication for Markov State Models Builder

MSMBuilder citation

PMCID: 5511175

[…] of the last 100 ns was used and aligned to the 7tm backbone for the water density calculations., to construct the transition pathways between the open and closed conformations, we used the msmbuilder 3.2.034, 35 program to build a reversible msm, from which the shortest transition pathways were computed based on the transition-path theory17, 36–38 (see supplementary information b). […]

MSMBuilder institution(s)
Department of Chemistry, Stanford University, Stanford, CA, USA; Program in Biophysics, Stanford University, Stanford, CA, USA; Memorial Sloan Kettering Cancer Center, New York, NY, USA; Department of Computer Science, Stanford University, Stanford, CA, USA; Department of Structural Biology, Stanford University, Stanford, CA, USA
MSMBuilder funding source(s)
This work received funding from NIH grants U19 AI109662 and 2R01GM062868 and support from NSF-MCB-0954714, from NSF GRFP (DGE-114747), from NIH grant P30CA008747, the Sloan Kettering Institute, and Starr Foundation grant I8-A8-058.

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