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


Matteo Tiberti, Wouter Boomsma, Tone Bengtsen




GNU Public License v3


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 [ᵃLindorff-Larsen2009]. The implementation and examples are described in [ᵃTiberti2015].

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 [ᵃTiberti2015]. Modules References


Kresten Lindorff-Larsen and Jesper Ferkinghoff-Borg. Similarity measures for protein ensembles. PLOS ONE, 4(1):1–13, 01 2009. doi:10.1371/journal.pone.0004203.


Matteo Tiberti, Elena Papaleo, Tone Bengtsen, Wouter Boomsma, and Kresten Lindorff-Larsen. Encore: software for quantitative ensemble comparison. PLOS Computational Biology, 11(10):1–16, 10 2015. doi:10.1371/journal.pcbi.1004415.