SuMo: A Tool for Protein Function Inference Based on 3D Structures Comparisons - Identification of Ligand Binding Site and Protein-Protein Interaction Area - page 20

Fig. 1.4 Superimposition, obtained by SuMo software, of the Penicillin Binding Protein (1QMF)
in blue with the beta - lactamase (1YLZ) protein in green. Sites are well superimposed
(RMSD = 2.17 Å)
at the surface of a protein (Doppelt-Azeroual et al. 2010 ) or Fragments-Based Drug
Design (Moriaud et al. 2009 ). A similar approach using clouds of atoms has been
recently described (Hoffmann et al. 2010 ) and today a database of protein com-
plexes suitable for a critical assessment of predicted interaction is available is avail-
able to check blind predictions (Janin et al. 2003 ; Janin 2010 ). In this chapter, we
describe a revised strategy to define standardized “SuMo objects” in order to
improve the quality of the results and to decrease the CPU time. Since the number
of objects has been decreased in this new set, this contributes to a simpler descrip-
tion of the molecules to be compared. This lead to better response time even if the
size of the PDB has dramatically increased (21339 protein structures in 2003 versus
68353 in June 2011). The results obtained by SuMo by using the new set of object
favorably compare with those obtained with the classical set. This is confirmed in
the comparative study that used the 2 standards protein test sets of the original study.
For example, 2 additional proteases were identified and 13 instead of 8 among 16
have been correctly assigned as serine proteases. Even more spectacular are the
results obtained with the Penicillin Binding Protein (PBP) and beta lactamases. The
two proteins families are well separated at the function level giving rise to two well