SuMo: A Tool for Protein Function Inference Based on 3D Structures Comparisons - Identification of Ligand Binding Site and Protein-Protein Interaction Area - page 7

Fig. 1.2 List of detected ligands binding sites

1.3 Results

A comparison of the results obtained with the original definition of objects and the
new one described herein is provided on two extreme examples in which the structure-
function relationship in these proteins is well-known. First the classical case of
convergent evolution of serine proteases illustrates the independence of the SuMo
method from fold and sequence similarities.
The second example illustrates over a larger test set the possible discrimination of
functional sites from non-functional sites in the legume lectins family, despite high
sequence similarity and good overall superimposition as indicated by low RMSD.

1.3.1 Test of New Set on Proteases

To perform this test a special set of models was made. From the PDB, 61 proteases
and 970 isomerases were downloaded. For the isomerase (EC 3.1.3) a second set was
made to be sure that there is no protease function in these isomerase. The first 970