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Table 6 Performance of all methods on the “hard” target proteins over each type of ligand

From: Protein ligand-specific binding residue predictions by an ensemble classifier

Ligand Na Method Accuracy (%) Sensitivity (%) Specificity (%) MCC (%)b
CU 3 TargetCom 98.76 16.67 1 23.42
COACH 98.76 16.67 1 23.42
S-SITE 98.76 33.33 99.56 27.04
TargetSeq 98.33 0 1 0
COFACTOR 98.33 0 1 0
TM-SITE 98.33 0 1 0
FE 3 TargetCom 98.48 16.67 1 23.39
COACH 98.48 16.67 1 23.39
S-SITE 98.73 25.00 1 28.76
TargetSeq 98.26 12.5 99.9 20.03
COFACTOR 97.98 0 1 0
TM-SITE 97.98 0 1 0
ZN 30 TargetCom 98.38 40.63 99.42 37.49
COACH 97.65 40.91 98.66 31.86
S-SITE 97.43 43.32 98.37 33.51
TargetSeq 97.97 7.02 99.68 11.43
COFACTOR 98.14 0 1 0
TM-SITE 97.99 0 99.85 −0.15
SO4 5 TargetCom 97.11 6.67 99.61 7.61
COACH 97.02 6.67 99.51 7.08
S-SITE 97.11 0 1 0
TargetSeq 97.11 0 1 0
COFACTOR 97.39 6.67 99.9 1
TM-SITE 97.02 6.67 99.51 7.08
PO4 8 TargetCom 97.68 4.17 99.59 4.52
COACH 97.54 05 99.43 2.9
S-SITE 97.81 0 99.76 −0.36
TargetSeq 98.08 13.39 99.66 12.98
COFACTOR 97.91 0 99.86 −0.17
TM-SITE 98.05 0 1 0
ATP 4 TargetCom 93.92 5 97.14 1.38
COACH 93.92 5 97.14 1.38
S-SITE 96.42 0 1 0
TargetSeq 97.32 27.08 99.85 33.79
COFACTOR 96.42 0 1 0
TM-SITE 93.69 5 96.9 1.19
HEME 9 TargetCom 92.74 16.7 99.21 25.02
COACH 91.8 03.98 99.3 07.3
S-SITE 92.43 14.9 99.2 17.25
TargetSeq 89.54 15.47 95.68 11.59
COFACTOR 92.12 0 1 0
TM-SITE 92.12 0 1 0
  1. aThe number of “hard” target proteins in each type of ligand
  2. bThe numbers shown in bold are the best values of the non-combination based method
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