Protein Binding Site Prediction
While there are many methods for predicting protein-protein interaction, very few can determine the specific site of interaction on each protein. Characterization of the specific sequence regions mediating interaction (binding sites) is crucial for an understanding of cellular pathways. Experimental methods often report false binding sites due to experimental limitations, while computational methods tend to require data which is not available at the proteome-scale. PIPE-Sites is a novel method for protein specific binding site prediction based on pairs of re-occurring polypeptide sequences, which have been previously shown to accurately predict protein-protein interactions. PIPE-Sites operates at high specificity and requires only the sequences of query proteins and a database of known binary interactions with no binding site data, making it applicable to binding site prediction at proteome-scale.
A.Amos-Binks*, C.Patulea*, S.Pitre, A.Schoenrock, Y.Gui, J.R.Green, A.Golshani, F.Dehne*, "Binding site prediction for protein-protein interactions and novel motif discovery using re-occurring polypeptide sequences", BMC Bioinformatics, 12:225, 2011 (Note: flagged by the publisher as 'highly accessed'). [pdf |link | pubmed]