4.2.6. ENCORE Ensemble Similarity Calculations — MDAnalysis.analysis.encore
- Author
Matteo Tiberti, Wouter Boomsma, Tone Bengtsen
- Year
2015-2017
- 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 [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:
Clustering based convergence evaluation :
ces_convergence()Dimensionality-reduction based convergence evaluation :
dres_convergence()
When using this module in published work please cite [ᵃTiberti2015].
4.2.6.1. Modules
- 4.2.6.1.1. Ensemble Similarity Calculations —
MDAnalysis.analysis.encore.similarity ces()ces_convergence()clustering_ensemble_similarity()cumulative_clustering_ensemble_similarity()cumulative_gen_kde_pdfs()dimred_ensemble_similarity()discrete_jensen_shannon_divergence()discrete_kullback_leibler_divergence()dres()dres_convergence()gen_kde_pdfs()harmonic_ensemble_similarity()hes()prepare_ensembles_for_convergence_increasing_window()write_output()- 4.2.6.1.2. Clustering
- 4.2.6.1.3. Dimensionality reduction
- 4.2.6.1.4. Distance Matrix calculation —
MDAnalysis.analysis.ensemble.confdistmatrix conformational_distance_matrix()get_distance_matrix()set_rmsd_matrix_elements()- 4.2.6.1.5. Covariance calculation —
encore.covariance covariance_matrix()ml_covariance_estimator()shrinkage_covariance_estimator()- 4.2.6.1.6. bootstrap procedures —
MDAnalysis.analysis.ensemble.bootstrap bootstrapped_matrix()get_distance_matrix_bootstrap_samples()get_ensemble_bootstrap_samples()- 4.2.6.1.7. Utility functions for ENCORE
4.2.6.2. References
- ᵃLindorff-Larsen2009
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.
- ᵃTiberti2015(1,2)
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.