InCa-SiteFinder: A method for structure-based prediction of inositol and carbohydrate binding sites on proteins

Carbohydrate binding sites are considered important for cellular recognition and adhesion and are important targets for drug design. In this paper we present a new method called InCa-SiteFinder for predicting non-covalent inositol and carbohydrate binding sites on the surface of protein structures. It uses the van der Waals energy of a protein–probe interaction and amino acid propensities to locate and predict carbohydrate binding sites. The protein surface is searched for continuous volume envelopes that correspond to a favorable protein–probe interaction. These volumes are subsequently analyzed to demarcate regions of high cumulative propensity for binding a carbohydrate moiety based on calculated amino acid propensity scores.InCa-SiteFinder1 was tested on an independent test set of 80 protein–ligand complexes. It efficiently identifies carbohydrate binding sites with high specificity and sensitivity. It was also tested on a second test set of 80 protein–ligand complexes containing 40 known carbohydrate binders (having 40 carbohydrate binding sites) and 40 known drug-like compound binders (having 58 known drug-like compound binding sites) for the prediction of the location of the carbohydrate binding sites and to distinguish these from the drug-like compound binding sites. At 73% sensitivity the method showed 98% specificity. Almost all of the carbohydrate and drug-like compound binding sites were correctly identified with an overall error rate of 12%.