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Information


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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Documentation


Maintainer


  • person_outline Vijay S. Pande

Publication for Markov State Models Builder

MSMBuilder citations

 (24)
library_books

How structural elements evolving from bacterial to human SLC6 transporters enabled new functional properties

2018
BMC Biol
PMCID: 5852957
PMID: 29540172
DOI: 10.1186/s12915-018-0495-6

[…] zed the reduced conformational space generated by the first two tICA reaction coordinates into 100 microstates (Additional file : Figure S11) using the K-means clustering algorithm implemented in the MSMBuilder3 software []. TPMs were constructed at several different lag times to obtain the implied time-scale plots shown in Additional file : Figure S10, so that the one in which Markovian behavior […]

library_books

Linking time series of single molecule experiments with molecular dynamics simulations by machine learning

2018
eLife
PMCID: 5933924
PMID: 29723137
DOI: 10.7554/eLife.32668.022

[…] s further characterized by calculating pfold, the probability of a given state to fold before it unfolds. The pfold was solved by applying the transition-path theory (; ) (with committors function in MSMBuilder []). The pfold was mapped onto geometric space (Cα-RMSDs of the hairpins 1 and 2) using the trajectories generated as described above.We conducted pathway analysis from the unfolded to the […]

library_books

Dynamics of the excised base release in thymine DNA glycosylase during DNA repair process

2017
Nucleic Acids Res
PMCID: 5778594
PMID: 29253232
DOI: 10.1093/nar/gkx1261

[…] ctive site.We then projected each SMD conformation onto the top four slowest tICs, followed by clustering the projected conformations into 100 classes using the K-centers algorithm implemented in the MSMbuilder package (,). Finally, from each cluster, the center conformation was selected as the representative structure for the subsequent unbiased MD simulations. […]

library_books

Millisecond dynamics of BTK reveal kinome wide conformational plasticity within the apo kinase domain

2017
Sci Rep
PMCID: 5688120
PMID: 29142210
DOI: 10.1038/s41598-017-10697-0

[…] time of 80 ns) from the Markovian transition matrix.The trajectories were featurized and analyzed using the MDTraj package while tICA dimensionality reduction and Markov modeling were performed using MSMBuilder. Most of the analysis was performed within the IPython/Jupyter scientific environment with extensive use of the matplotlib, and scikit-learn libraries. All protein images were generated usi […]

library_books

Similar Active Sites and Mechanisms Do Not Lead to Cross Promiscuity in Organophosphate Hydrolysis: Implications for Biotherapeutic Engineering

2017
J Am Chem Soc
PMCID: 5724027
PMID: 29113434
DOI: 10.1021/jacs.7b09384

[…] All simulation analysis was performed using the QCalc module of Q5.10 in combination with Qtools 0.5.10 (DOI: 10.5281/zenodo.842003), VMD 1.9.1, GROMACS 5.0.2, MDTraj, MSMBuilder, and PyMOL, as described in the Supporting Information. […]

library_books

Conformational Transitions of the Pituitary Adenylate Cyclase Activating Polypeptide Receptor, a Human Class B GPCR

2017
Sci Rep
PMCID: 5511175
PMID: 28710390
DOI: 10.1038/s41598-017-05815-x

[…] d trajectory 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 3.2.0, program to build a reversible MSM, from which the shortest transition pathways were computed based on the transition-path theory, – (see Supplementary Information B). In MSM, the ve […]

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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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