Analysis and prediction of carbohydrate binding sites

An analysis of the characteristic properties of sugar binding sites was per formed on a set of 19 sugar binding proteins. For each site six parameters were evaluated: solvation potential, residue propensity, hydrophobicity, pl anarity, protrusion and relative accessible surface area. Three of the para meters were found to distinguish the observed sugar binding sites from the other surface patches. These parameters were then used to calculate the pro bability for a surface patch to be a carbohydrate binding site. The predict ion was optimized on a set of 19 non-homologous carbohydrate binding struct ures and a test prediction was carried out on a set of 40 protein-carbohydr ate complexes. The overall accuracy of prediction achieved was 65%, Results were in general better for carbohydrate-binding enzymes than for the lecti ns, with a rate of success of 87%.