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 73

Fig. 4.12 Comparison of MCC and F-measure results for FMN-complexing proteins as reported
by SuMo

4.5.4 Analysis of Individual Cases

Table 4.1 lists proteins for which identification proved easy, as well as those for
which the programs produced poor results. Most proteins were correctly processed
by various tools although there are also cases where only a single program was able
to produce correct results. This section presents such proteins in more detail.
Correct NAD + binding site identification was most frequently obtained for 2JHF
(alcohol dehydrogenase EC 1.1.1.1.) Of all the tested tools only ConSurf was unable
to correctly process this protein, which suggests that the relevant binding site is
specific and non-conservative in character.
The numbers of unique NAD + binding pocket matches returned by each program
are as follows: CASTp - 7, PocketFinder - 3, QSiteFinder - 5, FOD - 6, SuMo - 8.
Corresponding values for FMN are: QSiteFinder - 2, PocketFinder - 3, FOD - 4,
SuMo - 5. All these results refer to the top 10 places on each ranking list.