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RING: networking interacting residues, evolutionary information and energetics in protein structures

2011; Oxford University Press; Volume: 27; Issue: 14 Linguagem: Inglês

10.1093/bioinformatics/btr191

1367-4811

Alberto J. M. Martín, Michele Vidotto, Filippo Boscariol, Tomás Di Domenico, Ian Walsh, Silvio C. E. Tosatto,

Computational Drug Discovery Methods

Abstract Motivation: 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. Availability: The RING server, supplementary methods, examples and tutorials are available for non-commercial use at URL: http://protein.bio.unipd.it/ring/. Contact: silvio.tosatto@unipd.it