{ "cells": [ { "cell_type": "markdown", "metadata": {}, "source": [ "# Calculating the Dimension Reduction Ensemble Similarity between ensembles\n", "\n", "Here we compare the conformational ensembles of proteins in four trajectories, using the dimension reduction ensemble similarity method.\n", "\n", "**Last executed:** Sep 25, 2020 with MDAnalysis 1.0.0\n", "\n", "**Last updated:** September 2020\n", "\n", "**Minimum version of MDAnalysis:** 1.0.0\n", "\n", "**Packages required:**\n", " \n", "* MDAnalysis (Michaud-Agrawal *et al.*, 2011, Gowers *et al.*, 2016)\n", "* MDAnalysisTests\n", "* [scikit-learn](https://scikit-learn.org/stable/)\n", " \n", "**Optional packages for visualisation:**\n", "\n", "* [matplotlib](https://matplotlib.org)\n", "\n", "\n", "