ROC analysis of binding site prediction using PSSMs against PDNA-RDN reference data set, compared with results obtained from sequence based predictions. The sensitivity of the prediction could be adjusted by changing the threshold on predicted probabilities, to annotate that residue to be DNA-binding or otherwise. As may be noted the area under the PSSM based prediction curve is significantly greater than that obtained from sequence based predictions. In addition, sensitivity versus specificity values also seems to be difficult to manipulate in case of sequence based predictions as points on the curve are very closely spaced. PDNA-RDN curve also shows the levels of prediction scores expected on our web-based predictions.