Prediction of Binding Sites in HCV Protein Complexes Using a Support Vector Machine
ICIC '08 Proceedings of the 4th international conference on Intelligent Computing: Advanced Intelligent Computing Theories and Applications - with Aspects of Theoretical and Methodological Issues
Patch prediction of protein interaction sites: validation of a scoring function for an online server
BIRD'07 Proceedings of the 1st international conference on Bioinformatics research and development
Protein surface characterization using an invariant descriptor
Journal of Biomedical Imaging - Special issue on Mathematical Methods for Images and Surfaces 2011
IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB)
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Summary: 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 Contact: s.jones@sussex.ac.uk