SHARP2:: protein-protein interaction predictions using patch analysis

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 (SHAW). Parameter scores for each patch are combined, and the patch with the highest combined score is predicted as a potential interaction site. SHAW 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.