title: RING: networking interacting residues, evolutionary information and energetics in protein structures.
abstract: BACKGROUND
  Residue interaction networks (RINs) have been used in the literature to describe the protein 3D structure as a graph where nodes represent residues and edges physico-chemical interactions, e.g. hydrogen bonds or van-der-Waals contacts. Topological network parameters can be calculated over RINs and have been correlated with various aspects of protein structure and function. Here we present a novel web server, RING, to construct physico-chemically valid RINs interactively from PDB files for subsequent visualization in the Cytoscape platform. The additional structure-based parameters secondary structure, solvent accessibility and experimental uncertainty can be combined with information regarding residue conservation, mutual information and residue-based energy scoring functions. Different visualization styles are provided to facilitate visualization and standard plugins can be used to calculate topological parameters in Cytoscape. A sample use case analyzing the active site of glutathione peroxidase is presented.
  
  
  BACKGROUND
  The RING server, supplementary methods, examples and tutorials are available for non-commercial use at URL: http://protein.bio.unipd.it/ring/.
authors.affiliation: Department of Biology, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy.
authors.forename: Alberto J M
authors.initials: AJ
authors.lastname: Martin
authors.forename: Michele
authors.initials: M
authors.lastname: Vidotto
authors.forename: Filippo
authors.initials: F
authors.lastname: Boscariol
authors.forename: Tomàs
authors.initials: T
authors.lastname: Di Domenico
authors.forename: Ian
authors.initials: I
authors.lastname: Walsh
authors.forename: Silvio C E
authors.initials: SC
authors.lastname: Tosatto
mesh_terms: D030562:Databases, Protein; D005979:Glutathione Peroxidase / Q000737:chemistry; D006801:Humans; D021621:Imaging, Three-Dimensional; D020407:Internet; D011487:Protein Conformation; D025941:Protein Interaction Mapping / Q000379:methods; D011506:Proteins / Q000737:chemistry* / Q000378:metabolism; D012984:Software
chemical_list: D011506:Proteins; D005979:Glutathione Peroxidase