SuMo: A Tool for Protein Function Inference Based on 3D Structures Comparisons - Identification of Ligand Binding Site and Protein-Protein Interaction Area - page 8

Fig. 1.3 Superimposition of hits in SuMo

entres from the PDB were downloaded and added to the database. For protease,
61 models were chosen and dispatched in several sub families: 16 serine proteases
(EC 3.4.21); 8 metallopeptidases (EC 3.4.24); 8 cysteine peptidases (3.4.22); 9 aspartic
peptidases (3.4.23); 4 aminopeptidases (EC 3.4.11); 6 metallocarboxypeptidase
(EC 3.4.17); 5 serine carboxypeptidases (EC 3.4.16); 1 cysteine carboxypeptidases
(EC 3.4.18) and 4 threonine peptidases (EC 3.4.25). The list of serine proteases was:
1A5H, 1BF9, 1BML, 1CEA, 1D3P, 1DDJ, 1EZX, 1FAX, 1FLE, 1FQ3, 1GI7, 1H4W,
1IAU, 1LTO, 1SBC and 1AFQ. The query was defined on the active site of the
1AFQ serine protease model (Kashima et al. 1998 ). SuMo objects were chosen
within three spheres of selection with 10 Å radius and centered on W212, F302 and
S218 residues. The selected set of objects to form the query is about 138 different
objects located on 58 residues.
The result of the run was analysed, the job takes less than 3 min of running time
on a quad cpu Xeon core. The first 13 hits were all serine proteases and the 1SBC
entry was found on rank 79, the 2 other last entres were not recovered. The result is
presented on Table 1.1 . Hits number 34, 37 and 39 were cysteine endo peptidases
with PDB code 1 AU0, 1MEM and 1KFU, respectively. 16 proteases among 61 were