Figure 5 illustrates the results of reliability scoring scheme applied in the Jnet method. Those residues predicted with a confidence of 5 or greater had an average Q3 accuracy of 84%, and covered 68% of the total residues. Figures 7 and 6 show a comparison of the reliability scores for Jnet and the PHD prediction algorithm. The greatest benefits in accuracy for the new Jnet method arise for those positions assigned to reliability scores below 5.