Comparison of template-based alignments with ProMOL, 3DMSS-Sites, and PDBSiteScan. Structures from each of the six EC classes were queried using ProMOL, 3DMSS-Sites, and PDBSiteScan. A match is based on the EC Class and residues described in the Catalytic Site Atlas. Level 1 matches shared the first 3 numbers in the EC class; level 2 matches shared all four EC class numbers and level 3 matches include level 2 matches that also share all active site residues. The reported percentages simply reflect the fraction of matches by each method for each EC class. The selection of structures for this test is described under Implementation. The distribution of structures follows: for EC1, a total of 26 query structures from 16 unique EC classes were queried using ProMOL, 3DMSS-Sites and PDBSiteScan. The test sets for the other classes were similar: EC2 (29, 18), EC3 (20, 12), EC4 (23, 13), EC5 (25, 8), EC6 (25, 7).