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 69

Fig. 4.8 Comparison of MCC and F-measure results for FMN-complexing proteins as reported by
PocketFinder
Differences in the validity of binding site identification for NAD + - and FMN-
complexing proteins are depicted in Figs. 4.15 and 4.16 respectively. We have
selected proteins which obtained a score of 0.8-1.0 on the MCC scale and a score
of 0.4-0.5 on the F-measure scale for FMN, as well as those with MCC values of
approximately 0.8 and F-measure values of approximately 0.4 for NAD + . The pre-
sented tables compare the scores obtained for each of those proteins using various
theoretical models. As can be seen, different tools exhibit varying degrees of accu-
racy in identifying specific binding pockets.
An interesting conclusion arises with respect to FMN complexation sites: in this
scope all of the analyzed software packages seem to have arrived at an identical set
of “difficult” proteins, while also producing consistent results for “easy” ones.
Result sets obtained from ConSurf and CASTp contained no unique matches. Thus,
both packages can be described as relatively trustworthy but also largely incapable
of handling unusual situations.