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.
Original language | English |
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Article number | btr191 |
Pages (from-to) | 2003-2005 |
Number of pages | 3 |
Journal | Bioinformatics |
Volume | 27 |
Issue number | 14 |
DOIs | |
State | Published - 2011 |
Externally published | Yes |
Bibliographical note
Funding Information:Funding: University of Padova (grants CPDA098382, CPDR097328 to S.T.); FIRB Futuro in Ricerca (grant RBFR08ZSXY to S.T.).
ASJC Scopus subject areas
- Statistics and Probability
- Biochemistry
- Molecular Biology
- Computer Science Applications
- Computational Theory and Mathematics
- Computational Mathematics