RING: networking interacting residues, evolutionary information and energetics in protein structures.
Bioinformatics
; 27(14): 2003-5, 2011 Jul 15.
Article
em En
| MEDLINE
| ID: mdl-21493660
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/.
Texto completo:
1
Coleções:
01-internacional
Base de dados:
MEDLINE
Assunto principal:
Software
/
Proteínas
/
Internet
/
Bases de Dados de Proteínas
Limite:
Humans
Idioma:
En
Revista:
Bioinformatics
Assunto da revista:
INFORMATICA MEDICA
Ano de publicação:
2011
Tipo de documento:
Article
País de afiliação:
Itália