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Table 5 Average AUCs on the “25conf” dataset

From: A rotation-translation invariant molecular descriptor of partial charges and its use in ligand-based virtual screening

target (L/D) ACPC1 c ACPC25 c ACPC Pharao MACCS Shape-it ES3DH ES3D Gpi3 pi3 pi4 TAD TAT TGD TGT
ace (1140/43653) 0.49 0.48 0.45 0.58 0.68 0.57 0.34 0.44 0.72 0.60 0.62 0.61 0.57 0.49 0.60
ache (2450/89138) 0.80 0.80 0.80 0.69 0.72 0.69 0.48 0.28 0.81 0.85 0.85 0.66 0.75 0.60 0.74
ada (876/18697) 0.82 0.81 0.78 0.66 0.80 0.64 0.71 0.42 0.81 0.75 0.74 0.84 0.82 0.85 0.87
alr2 (348/16063) 0.60 0.59 0.47 0.74 0.42 0.52 0.35 0.33 0.54 0.66 0.64 0.32 0.24 0.29 0.44
ampc (507/15069) 0.84 0.83 0.89 0.86 0.88 0.71 0.82 0.59 0.87 0.87 0.90 0.75 0.83 0.84 0.75
ar (363/42557) 0.75 0.73 0.72 0.67 0.80 0.75 0.68 0.44 0.71 0.76 0.71 0.81 0.66 0.80 0.67
cdk2 (1138/43682) 0.88 0.88 0.93 0.62 0.49 0.54 0.42 0.50 0.66 0.68 0.67 0.34 0.41 0.34 0.46
comt (124/7148) 0.83 0.81 0.80 0.81 0.77 0.65 0.38 0.34 0.76 0.62 0.75 0.43 0.46 0.46 0.53
cox1 (422/15672) 0.30 0.29 0.27 0.55 0.51 0.46 0.47 0.38 0.50 0.40 0.48 0.49 0.61 0.50 0.64
cox2 (6483/270311) 0.94 0.94 0.87 0.46 0.15 0.16 0.62 0.52 0.22 0.26 0.33 0.49 0.50 0.65 0.74
dhfr (9550/166944) 1.00 1.00 1.00 0.94 0.96 0.56 0.63 0.46 0.98 0.93 0.98 0.99 1.00 0.98 0.91
egfr (9964/337283) 0.91 0.89 0.90 0.96 0.78 0.57 0.49 0.25 0.89 0.69 0.89 0.50 0.66 0.46 0.53
er+ (289/39507) 0.92 0.91 0.94 0.81 0.95 0.63 0.26 0.38 0.76 0.89 0.68 0.96 0.96 0.96 0.96
er- (975/32961) 0.62 0.60 0.71 0.75 0.89 0.66 0.29 0.40 0.83 0.84 0.69 0.95 0.92 0.95 0.92
fgfr1 (2360/106612) 0.93 0.94 0.87 0.54 0.55 0.63 0.61 0.41 0.79 0.59 0.49 0.37 0.49 0.36 0.50
fxa (3647/123379) 0.89 0.89 0.64 0.61 0.48 0.40 0.39 0.42 0.42 0.40 0.44 0.24 0.42 0.29 0.30
gart (775/20938) 1.00 1.00 1.00 0.94 0.98 0.69 0.89 0.89 0.97 0.97 0.98 0.98 0.98 0.96 0.98
gpb (845/44604) 0.97 0.96 0.87 0.23 0.68 0.42 0.24 0.29 0.34 0.16 0.32 0.18 0.20 0.17 0.16
gr (553/56086) 0.73 0.72 0.75 0.75 0.86 0.55 0.50 0.48 0.79 0.82 0.85 0.64 0.67 0.62 0.60
hivpr (1404/44909) 0.72 0.72 0.79 0.73 0.47 0.74 0.63 0.56 0.44 0.42 0.53 0.92 0.93 0.90 0.92
hivrt (822/32688) 0.86 0.86 0.82 0.47 0.43 0.28 0.55 0.47 0.47 0.57 0.51 0.31 0.39 0.39 0.34
hmga (814/33684) 0.89 0.89 0.87 0.83 0.94 0.85 0.57 0.53 0.94 0.93 0.94 0.99 0.98 0.97 0.98
hsp90 (572/20983) 0.58 0.56 0.67 0.81 0.70 0.58 0.84 0.59 0.93 0.89 0.79 0.52 0.66 0.58 0.61
inha (1782/71064) 0.58 0.58 0.59 0.48 0.78 0.48 0.24 0.30 0.33 0.35 0.36 0.41 0.66 0.49 0.71
mr (79/10177) 0.73 0.70 0.54 0.18 0.69 0.72 0.82 0.60 0.75 0.65 0.48 0.49 0.43 0.46 0.58
na (987/44278) 0.92 0.92 0.93 0.79 0.91 0.39 0.37 0.33 0.87 0.79 0.84 0.72 0.88 0.74 0.72
p38 (7014/186992) 0.54 0.51 0.57 0.89 0.76 0.69 0.62 0.38 0.87 0.82 0.88 0.48 0.60 0.38 0.59
parp (245/12871) 0.97 0.97 0.99 0.93 0.93 0.73 0.55 0.53 0.97 0.93 0.96 0.83 0.89 0.74 0.89
pde5 (1751/48431) 0.66 0.65 0.75 0.67 0.68 0.69 0.39 0.44 0.67 0.62 0.67 0.31 0.35 0.36 0.34
pdgfrb (3206/134591) 0.51 0.52 0.49 0.46 0.49 0.61 0.57 0.49 0.62 0.44 0.42 0.34 0.46 0.36 0.50
pnp (560/16694) 0.99 0.98 0.99 0.95 0.90 0.63 0.36 0.52 0.90 0.76 0.91 0.82 0.86 0.87 0.91
ppar γ (2010/65783) 0.91 0.90 0.88 0.89 0.89 0.70 0.21 0.25 0.92 0.94 0.92 0.86 0.94 0.76 0.86
pr (178/15966) 0.70 0.70 0.37 0.37 0.48 0.67 0.30 0.19 0.73 0.76 0.56 0.61 0.66 0.64 0.63
rxr α (392/17243) 0.77 0.77 0.86 1.00 0.99 0.70 0.53 0.49 0.95 0.97 0.99 0.94 0.95 0.99 0.90
sahh (586/25622) 0.98 0.98 0.96 0.57 0.97 0.71 0.78 0.65 0.96 0.93 0.95 0.89 0.95 0.90 0.96
src (2945/145751) 0.90 0.90 0.81 0.51 0.47 0.65 0.69 0.53 0.60 0.43 0.36 0.30 0.41 0.26 0.40
thrombin (1576/57564) 0.87 0.88 0.95 0.74 0.51 0.65 0.54 0.58 0.65 0.48 0.36 0.71 0.68 0.62 0.66
tk (379/15017) 0.98 0.98 0.98 0.84 0.92 0.54 0.47 0.37 0.89 0.86 0.87 0.86 0.86 0.85 0.89
trypsin (1128/39065) 0.90 0.90 0.98 0.64 0.29 0.45 0.46 0.28 0.30 0.29 0.41 0.72 0.80 0.69 0.81
vegfr2 (1604/66098) 0.79 0.78 0.67 0.47 0.42 0.44 0.32 0.24 0.57 0.54 0.48 0.37 0.41 0.33 0.38
Average 0.80 0.79 0.78 0.68 0.70 0.59 0.51 0.44 0.72 0.68 0.68 0.62 0.67 0.62 0.67
Median 0.85 0.84 0.81 0.71 0.74 0.63 0.49 0.44 0.76 0.72 0.69 0.62 0.66 0.62 0.67
|Best method| N/A N/A 17 5 3 0 1 0 3 3 2 4 4 2 3
  1. For each of the 40 targets, the query was the last ligand in the ligands list of each target. For each target, the maximum AUC reached is underlined and in bold font. L = number of ligands; D = number of decoys. The ACPC1c and ACPC25c columns were computed and added for comparison. ACPC1c (resp. ACPC25c) shows the average AUC reached when using all active ligands as queries for ACPC on “1conf” (resp. “25conf”). Their |best method | cells were not filled in since they concern different experiments than other columns.