We are constructing a new protein functional site benchmark that includes several different types of functional site definitions. In the alpha-version of the Catalog of Important Sites (CIS), we include three different functional site definitions. Specifically, the CIS is based on a structurally nonredundant subsection of the Catalytic Site Atlas (CSA) (Porter, et al., 2004), meaning every member of the benchmark is assured to have at least one catalytic residue (as defined by the CSA). Catalytic residues are generally very well conserved, whereas other positions within the active site region can be more variable. To test for ability to predict which positions define active site structure, we have identified all residues contacting the catalytic residues using HBPLUS (McDonald and Thornton, 1994). The union of these secondary catalytic sites and the CSA catalytic residues define the active site benchmark. Finally, ligand-binding sites are defined by identifying (also with HBPLUS) all enzyme-ligand interactions.

If you use this dataset, please cite: KC DB and Livesay DR (2008). Improving position specific predictions of protein functional sites using phylogenetic motifs. Bioinformatics, In press.

To download the CIS, please click here.