title: MDN: A Web Portal for Network Analysis of Molecular Dynamics Simulations.
abstract: 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 can identify residues that are important for signal propagation, as well as measure the efficiency of signal propagation by calculating the network coupling. This tool, called MDN, was used to characterize signal propagation in Escherichia coli heat-shock protein 70-kDa. Two variants of this protein experimentally shown to be allosterically active exhibit higher network coupling relative to that of 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.
authors.affiliation: Department of Chemical Engineering, Columbia University, New York, New York.
authors.forename: Andre A S T
authors.initials: AA
authors.lastname: Ribeiro
authors.affiliation: Department of Chemical Engineering, Columbia University, New York, New York. Electronic address: vortiz@columbia.edu.
authors.forename: Vanessa
authors.initials: V
authors.lastname: Ortiz
mesh_terms: D000494:Allosteric Regulation; D055808:Drug Discovery / Q000379:methods; D004926:Escherichia coli; D029968:Escherichia coli Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D018840:HSP70 Heat-Shock Proteins / Q000737:chemistry / Q000235:genetics / Q000378:metabolism; D020407:Internet; D056004:Molecular Dynamics Simulation; D009154:Mutation; D015398:Signal Transduction; D012984:Software
chemical_list: D029968:Escherichia coli Proteins; D018840:HSP70 Heat-Shock Proteins; C063842:dnaK protein, E coli