Provides code to analyze molecular dynamics simulations and identify correlated motions and potential allosteric networks, and to compare conformational ensembles from molecular dynamics simulations to identify dihedral population shifts
MutInf is an analysis package written in Python. inline C, and R that analyses data from Molecular Dynamics Simulations to identify statistically significant correlated motions and calculate residue-by-residue conformational entropies. Our work has shown that the pattern of mutual information between residues can be used to predict potential allosteric sites, identify couplings between allosteric sites, and identify residues that might be important in mediating these couplings.
Recently, we've also included a module to compare conformational ensembles from MD sims or sets of MD sims using the Kullback-Leibler Divergence / Jensen-Shannon Divergence expansion. This is useful for comparing simulations of wildtype/mutant proteins, apo/holo, simulations started from different conformations, etc. Please see McClendon et. al., JCTC, 2012. for more information.
Sep 29, 2016