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Bioinformatics. 2011 Jul 15;27(14):2003-5. doi: 10.1093/bioinformatics/btr191. Epub 2011 Apr 14.

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

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  • 1Department of Biology, University of Padova, Viale G. Colombo 3, 35131 Padova, Italy.

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/.

PMID:
21493660
DOI:
10.1093/bioinformatics/btr191
[PubMed - indexed for MEDLINE]
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