Sharp2: Protein-protein Interaction Predictions Using Patch Analysis.
From: Department of Biochemistry, School of Life Sciences, John Maynard Smith Building, University of Sussex, Falmer, Brighton, BN1 9QG, UK.
Bioinformatics (Oxford, England)
- Publish Date: Jul 2006
- ISSN: 1460-2059
- Volume: 22
- Issue: 14
- Pages: 1794-5
- Medium: Internet
- Language: English
- Citation (JAMA): Murakami Yoichi, Jones Susan, et al. Sharp2: Protein-protein Interaction Predictions Using Patch Analysis.. Bioinformatics Jul 2006;22:1794-5
Abstract
SHARP2 is a flexible web-based bioinformatics tool for predicting potential protein-protein interaction sites on protein structures. It implements a predictive algorithm that calculates multiple parameters for overlapping patches of residues on the surface of a protein. Six parameters are calculated: solvation potential, hydrophobicity, accessible surface area, residue interface propensity, planarity and protrusion (SHARP2). Parameter scores for each patch are combined, and the patch with the highest combined score is predicted as a potential interaction site. SHARP2 enables users to upload 3D protein structure files in PDB format, to obtain information on potential interaction sites as downloadable HTML tables and to view the location of the sites on the 3D structure using Jmol. The server allows for the input of multiple structures and multiple combinations of parameters. Therefore predictions can be made for complete datasets, as well as individual structures. AVAILABILITY: http://www.bioinformatics.sussex.ac.uk/SHARP2.
Mesh Headings (Keywords): Algorithms, Amino Acid Sequence, Binding Sites, Computer Simulation, Models, Chemical, Models, Molecular, Molecular Sequence Data, Protein Binding, Protein Interaction Mapping, Proteins, Sequence Analysis, Protein, Software, User-Computer Interface
Check for Full Text / PubMed Unique Identifier (PMID): 16672257
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