title: WebPSN: a web server for high-throughput investigation of structural communication in biomacromolecules.
abstract: We developed a mixed Protein Structure Network (PSN) and Elastic Network Model-Normal Mode Analysis (ENM-NMA)-based strategy (i.e. PSN-ENM) to investigate structural communication in biomacromolecules. The approach starts from a Protein Structure Graph and searches for all shortest communication pathways between user-specified residues. The graph is computed on a single preferably high-resolution structure. Information on system's dynamics is supplied by ENM-NMA. The PSN-ENM methodology is made of multiple steps both in the setup and analysis stages, which may discourage inexperienced users. To facilitate its usage, we implemented WebPSN, a freely available web server that allows the user to easily setup the calculation, perform post-processing analyses and both visualize and download numerical and 3D representations of the output. Speed and accuracy make this server suitable to investigate structural communication, including allosterism, in large sets of bio-macromolecular systems.
  
  
  METHODS
  The WebPSN server is freely available at http://webpsn.hpc.unimore.it.
authors.affiliation: Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 183, 41125 Modena, Italy.
authors.forename: Michele
authors.initials: M
authors.lastname: Seeber
authors.affiliation: Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 183, 41125 Modena, Italy.
authors.forename: Angelo
authors.initials: A
authors.lastname: Felline
authors.affiliation: Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 183, 41125 Modena, Italy.
authors.forename: Francesco
authors.initials: F
authors.lastname: Raimondi
authors.affiliation: Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 183, 41125 Modena, Italy.
authors.forename: Simona
authors.initials: S
authors.lastname: Mariani
authors.affiliation: Department of Life Sciences, University of Modena and Reggio Emilia, via Campi 183, 41125 Modena, Italy.
authors.forename: Francesca
authors.initials: F
authors.lastname: Fanelli
mesh_terms: D057166:High-Throughput Screening Assays; D006801:Humans; D020407:Internet; D056004:Molecular Dynamics Simulation; D054730:Protein Interaction Domains and Motifs; D011506:Proteins / Q000737:chemistry*; D016415:Sequence Alignment; D020539:Sequence Analysis, Protein / Q000379:methods*; D012984:Software; D040681:Structural Homology, Protein
chemical_list: D011506:Proteins