This upload contains python and R code used to analyse the covariance structure of proteins. It supports creating coarse grained elastic network models from PDB files, constructing covariance matrices from Molecular Dynamics trajectories, and quantifying and visualizing similarities of covariance matrices. This code was used to perform the analysis published in Fuglebakk et al. JCTC 2013 (listed under Related/alternate identifiers). The archive also contains parameter files for some of the Molecular Dynamics simulations analysed in Fuglebakk et al., and processed trajectory files containing alpha carbon positions superimposed on starting configuration for the simulation of: lysozyme, ATCase, myoglobin, trio and human prion protein.