(231c) Mdn: A Web Portal for Network Analysis of Molecular Dynamics Simulations

We introduce a web portal that employs network theory for the analysis of trajectories from molecular dynamics simulations. Users can create protein energy networks following methodology previously introduced by our group, and identify residues that are important for signal propagation, as well as measure the efficiency of signal propagation by calculating the network coupling. This new tool, called MDN, was used to characterize signal propagation in E. coli heat shock protein 70-kDa (DnaK). Two DnaK variants, experimentally shown to be allosterically active, exhibit higher network coupling than two inactive variants. In addition, calculations of partial coupling suggest that this quantity could be used as part of the criteria to determine ‘pocket druggability’ in drug discovery studies.