Prediction of catalytic residues based on an overlapping amino acid classification

Protein sequence conservation is a powerful and widely used indicator for predicting catalytic residues from enzyme sequences. In order to incorporate amino acid similarity into conservation measures, one attempt is to group amino acids into disjoint sets. In this paper, based on the overlapping amino acids classification proposed by Taylor, we define the relative entropy of Venn diagram (RVD) and RVD2. In large-scale testing, we demonstrate that RVD and RVD2 perform better than many existing conservation measures in identifying catalytic residues, especially than the commonly used relative entropy (RE) and Jensen–Shannon divergence (JSD). To further improve RVD and RVD2, two new conservation measures are obtained by combining them with the classical JSD. Experimental results suggest that these combination measures have excellent performances in identifying catalytic residues.