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MSMExplorer: visualizing Markov state models for biomolecule folding simulations
Open accessAbstract
Summary: Markov state models (MSMs) for the study of biomolecule folding simulations have emerged as a powerful tool for computational study of folding dynamics. MSMExplorer is a visualization application purpose-built to visualize these MSMs with an aim to increase the efficacy and reach of MSM science. Availability: MSMExplorer is available for download from https://simtk.org/home/msmexplorer. The source code is made available under the GNU Lesser General Public License at https://github.com/SimTk/msmexplorer. Contact: pande@stanford.edu
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MSMExplorer allows visualization of MSMs using graph and network diagrams, scatterplots of state properties, and interactive structure visualization.
“The MSMExplorer software package [https://simtk.org/home/msmexplorer] allows for the visualization of MSMs using graph and network diagrams, scatterplots of state properties, and interactive structure visualization [39].”
From Markov state models of biomolecular conformational dynamics (2014) · cites this paper as [39]
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EMMA: A Software Package for Markov Model Building and Analysis
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Markov state models of biomolecular conformational dynamics
Chodera, J. D., & Noé, F. (2014) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2014.04.002 · Cited by 776
Verkhivker, G. M., Agajanian, S., Hu, G., & Tao, P. (2020) · Frontiers in Molecular Biosciences · doi:10.3389/fmolb.2020.00136 · Cited by 76
Metadata
- Authors
- Cronkite-Ratcliff, B., & Pande, V.
- Affiliations
- Stanford University (US)
- Corresponding author
- Cronkite-Ratcliff, Bryce
- ORCID
- Pande, Vijay
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2013-01-30
- Volume
- 29
- Issue
- 7
- Pages
- 950-952
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2140796042
- Cited by
- 25
- References
- 1
- Citations by year
- 2025: 1 · 2024: 1 · 2022: 1 · 2021: 1 · 2020: 3 · 2019: 1 · 2018: 3 · 2017: 4 · 2016: 2 · 2015: 2 · 2014: 3 · 2013: 3
- FWCI
- 1.49
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Bioinformatics (publishedVersion)
- PubMed (publishedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Protein Structure and Dynamics
- Physical Sciences › Chemistry › Physical and Theoretical Chemistry › Advanced Physical and Chemical Molecular Interactions
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › RNA and protein synthesis mechanisms
- Keywords
- Markov state models, folding dynamics, protein folding simulation, conformational dynamics
- MeSH terms
- Computer Graphics, Computer Simulation, Markov Chains, Molecular Conformation, Software
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