The DOI matches its Crossref record; 2 of the 2 references it cites were found in a registry or an index.
Using generalized ensemble simulations and Markov state models to identify conformational states
Open accessAbstract
Part of understanding a molecule’s conformational dynamics is mapping out the dominant metastable, or long lived, states that it occupies. Once identified, the rates for transitioning between these states may then be determined in order to create a complete model of the system’s conformational dynamics. Here we describe the use of the MSMBuilder package (now available at https://simtk.org/home/msmbuilder/) to build Markov State Models (MSMs) to identify the metastable states from Generalized Ensemble (GE) simulations, as well as other simulation datasets. Besides building MSMs, the code also includes tools for model evaluation and visualization.
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Cites
Robust Perron cluster analysis in conformation dynamics
Deuflhard, P., & Weber, M. (2005) · Linear Algebra and its Applications · doi:10.1016/j.laa.2004.10.026 · Cited by 506
Coarse master equations for peptide folding dynamics
Buchete, N.-V., & Hummer, G. (2008) · The Journal of Physical Chemistry B · doi:10.1021/jp0761665 · Cited by 477
Cited by
Everything you wanted to know about Markov State Models but were afraid to ask
Pande, V. S., Beauchamp, K., & Bowman, G. R. (2010) · Methods · doi:10.1016/j.ymeth.2010.06.002 · Cited by 698
Self-citationMolecular Simulation of ab Initio Protein Folding for a Millisecond Folder NTL9(1−39)
Voelz, V. A., Bowman, G. R., Beauchamp, K., & Pande, V. S. (2010) · Journal of the American Chemical Society · doi:10.1021/ja9090353 · Cited by 503
Self-citationWei, G., Xi, W., Nussinov, R., & Ma, B. (2016) · Chemical Reviews · doi:10.1021/acs.chemrev.5b00562 · Cited by 436
To milliseconds and beyond: challenges in the simulation of protein folding
Lane, T. J., Shukla, D., Beauchamp, K. A., & Pande, V. S. (2013) · Current Opinion in Structural Biology · doi:10.1016/j.sbi.2012.11.002 · Cited by 409
Self-citationBowman, G. R., Beauchamp, K. A., Boxer, G., & Pande, V. S. (2009) · The Journal of Chemical Physics · doi:10.1063/1.3216567 · Cited by 396
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Metadata
- Authors
- Bowman, G. R., Huang, X., & Pande, V. S.
- Venue
- Methods
- Publisher
- Elsevier BV
- Published
- 2009-10
- Volume
- 49
- Issue
- 2
- Pages
- 197-201
- ISSN
- 1046-2023 (ISSN-L)
- OpenAlex
- W2066795144
- Cited by
- 302
- References
- 2
- FWCI
- 5.28
- Type
- journal article
- Language
- en
- Open access
- green
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