## PyEMMA specifications

### Information

 Unique identifier OMICS_15117 PyEMMA Package/Module Graphical user interface None Unix/Linux, Mac OS, Windows C, Python GNU Lesser General Public License version 3.0 Medium 2.3 Stable C/C++ compiler, setuptools, cython, numpy, scipy, matplotlib Yes

### Maintainer

• person_outline Frank Noé <>

## Publication for PyEMMA

library_books

### PyEMMA 2: A Software Package for Estimation, Validation, and Analysis of Markov Models.

2015 J Chem Theory Comput
PMID: 26574340

## PyEMMA in publications

(18)
library_books

### Molecular details of dimerization kinetics reveal negligible populations of transient µ opioid receptor homodimers at physiological concentrations

PMCID: 5955887
PMID: 29769636
DOI: 10.1038/s41598-018-26070-8

[…] clusters, it cannot transition into another one without first passing through the unbound cluster. k-means clustering, transition matrix estimation and spectral clustering were performed using pyemma (version 2.3) python functions., to aid convergence of the free-energy and kinetic estimation, umbrella sampling runs were performed restraining the system around selected k-mean centers. […]

library_books

### Examining a Thermodynamic Order Parameter of Protein Folding

PMCID: 5940758
PMID: 29740018
DOI: 10.1038/s41598-018-25406-8

[…] \setlength{\oddsidemargin}{-69pt} \begin{document}$${g}_{u}^{{\rm{solv}}}$$\end{document}gusolv, we employed the 3d-rism theory, whose details are provided in supplementary methods., we employed pyemma 2 for carrying out the steps in the msm construction. the raw cartesian coordinates in the simulation trajectory of hp35, taken with a 1 ns interval here, were first represented by the cosines […]

library_books

### Live Observation of Two Parallel Membrane Degradation Pathways at Axon Terminals

PMCID: 5944365
PMID: 29551411
DOI: 10.1016/j.cub.2018.02.032

[…] on this volume [, ]. areas with high correlation were traced to extract the compartment trajectories. to analyze the trajectories from the image analysis, a markov state model (msm) was defined with pyemma 2.4 [], where each state represents an area of 8×8 pixels (600 states in a 60 by 10 grid). the state assignment for each compartment was computed with the negative exponential distance […]

library_books

### DNA sliding in nucleosomes via twist defect propagation revealed by molecular simulations

PMCID: 5887990
PMID: 29506273
DOI: 10.1093/nar/gky158

[…] reveals that these are the slowest-changing dna contacts and are therefore sufficient to produce a minimal model of 601 repositioning., markov state models were generated using the software pyemma 2 (). for each periodic sequence we produced a bayesian msm using 24, 24, 36, 36, 12 and 12 independent trajectories (107 md steps each) and a lag time of 0.04, 0.1, 0.1, 0.02, 2 and 2 × 106 […]

library_books

### Structural and biochemical characterization of the biuret hydrolase (BiuH) from the cyanuric acid catabolism pathway of Rhizobium leguminasorum bv. viciae 3841

PMCID: 5806882
PMID: 29425231
DOI: 10.1371/journal.pone.0192736

[…] to further analysis via conformational clustering using the k-means algorithm with k = 20. these states were then assembled into a markovian state model with a lag time of 40 nanoseconds using the pyemma python library []. the caver algorithm [,] was used to identify a number of transiently forming tunnels linking the active sites of each monomer to the surface as well as the central cavity […]

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PyEMMA institution(s)
Department for Mathematics and Computer Science, Freie Universitat, Berlin, Germany
PyEMMA funding source(s)
This work was supported by ERC starting grant pcCell, FU Berlin startup funds, Deutsche Forschungsgemeinschaft Grant Nos. 825/3-1 and SFB 1114, and Einstein Foundation Berlin, SoOPiC.

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