4.2.6. ENCORE Ensemble Similarity Calculations — MDAnalysis.analysis.encore

Author:Matteo Tiberti, Wouter Boomsma, Tone Bengtsen
Copyright:GNU Public License v3
Maintainer:Matteo Tiberti <matteo.tiberti@gmail.com>, mtiberti on github

New in version 0.16.0.

The module contains implementations of similarity measures between protein ensembles described in [Lindorff-Larsen2009a]. The implementation and examples are described in [Tiberti2015a].

The module includes facilities for handling ensembles and trajectories through the Universe class, performing clustering or dimensionality reduction of the ensemble space, estimating multivariate probability distributions from the input data, and more. ENCORE can be used to compare experimental and simulation-derived ensembles, as well as estimate the convergence of trajectories from time-dependent simulations.

ENCORE includes three different methods for calculations of similarity measures between ensembles implemented in individual functions:

  • Harmonic Ensemble Similarity : hes()
  • Clustering Ensemble Similarity : ces()
  • Dimensional Reduction Ensemble Similarity : dres()

as well as two methods to evaluate the convergence of trajectories:

When using this module in published work please cite [Tiberti2015a]. References

[Lindorff-Larsen2009a]Similarity Measures for Protein Ensembles. Lindorff-Larsen, K. Ferkinghoff-Borg, J. PLoS ONE 2008, 4, e4203.
[Tiberti2015a](1, 2) ENCORE: Software for Quantitative Ensemble.. Comparison. Matteo Tiberti, Elena Papaleo, Tone Bengtsen, Wouter Boomsma, Kresten Lindorff- Larsen. PLoS Comput Biol. 2015, 11, e1004415