Comparative Analysis of Techniques Oriented on the Recognition of Ligand Binding Area in Proteins - Identification of Ligand Binding Site and Protein-Protein Interaction Area - page 72

Fig. 4.11 Comparison of MCC and F-measure results for FMN-complexing proteins as reported
by the FOD model
The group of “easy” proteins complexing NAD + (shown in Table 4.4 ) reveals
more common characteristics suggesting that probably the dimeric proteins of the
class EC.1.1.1.1 (oxydoreductase) represent the structures with well defined ligand
binding cavity.
The “hard” proteins (in respect to NAD + binding side identification) appeared
to be all enzymes of bacterial origin (except one protein which is mammalian).
No common characteristics can be given in this point to make predictable the
success or failure in identification (Table 4.5 ). The characteristics of cavities for
“easy” and “hard” proteins is given in Table 4.6 .
Table 4.6 reveals the general difference in NAD + and FMN binding cavity which
is much larger for NAD + although the other parameters seem to be quite comparable
for these two ligands. The comparison between “easy” and “hard” reveals differences
of vertices, buried vertices and average depth which are lower for FMN binding
cavities in proteins recognized as “hard”.