Figure 3

Accuracy of functional site identification by the HMM-derived entropy method, the HMM-derived relative entropy method, three AL2CO-based methods (AL2CO_entropy, AL2CO_variance and AL2CO_sop) and the SCORECONS method on the Thornton and Lovell datasets. The average ROC score and the top 10 hits score are used to evaluate performance. The HMM-derived relative entropy method has the best performance, demonstrating the importance of using background frequency information, as well as accurate estimates of amino acid frequencies.