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 66

Fig. 4.5 Comparison of MCC and F-measure results for NAD + -complexing proteins as reported
by the FOD model. The cutoff threshold was established at 80 %, meaning that only values beyond
80 % of the maximum were considered valid

The PocketFinder tool also produced high MCC values for most of the tested
proteins, with only two molecules ranked below 0 (Fig. 4.8 ). As with most other
software packages, F-measure scores are somewhat more diverse than MCC results,
although they remain comparable (falling between 0.2 and 0.3 in most cases).
The QSiteFinder tool identified a relatively numerous group of proteins with
high MCC and F-measure scores - notably a set of molecules for which MCC values
are in the 0.4-1.0 range (Fig. 4.9 ). These results are supported by the corresponding
F-measure scores.

4.5.2.2 Knowledge-Based Packages

Consistent F-measure results were obtained by applying the ConSurf package.
Good agreement between MCC and F-measure scores indicates high reliability
of evolutionary methods in the context of FMN-complexing proteins (Fig. 4.10 ).