Skip to main content
. 2016 Jul 4;10:2137–2154. doi: 10.2147/DDDT.S108118

Table 2.

Summary of performances of pharmacophore models in virtual screening study

PDB code Actives Decoys Hit rate Total hits TP FP TN
1IEP 45 2,250 0.52 12 9 3 2,247
2JDO 19 950 16.41 159 4 155 795
2XMY 14 700 4.20 30 7 23 677
3E37a 10 500 40.78 208 6 202 298
3E37b 10 500 44.71 228 5 223 277
3E37c 10 500 10.98 56 2 54 446
3PE1d 274 15,250 4.31 669 206 463 14,780
3PE1e 274 15,250 0.30 47 41 6 15,237
3PE2 274 15,250 6.19 960 11 949 14,294
4ACM 42 2,150 3.51 77 23 54 2,096
4BBGf 76 3,800 3.12 121 48 73 3,726
4BBGg 76 3,800 2.40 93 45 48 3,751
4BBGh 76 3,800 4.02 156 63 93 3,706
4PK5i 29 1,450 5.34 79 6 73 1,377
4PK5j 29 1,450 5.47 81 6 75 1,375
FN Ya % yield Se Sp EF GH
1IEP 36 75.00 20 0.20 0.99 3,825 0.75*
2JDO 15 2.51 21 0.21 0.84 128 0.32
2XMY 7 23.33 50 0.50 0.97 1,190 0.58*
3E37a 4 2.88 60 0.60 0.60 147 0.93*
3E37b 5 2.19 50 0.50 0.55 112 0.79*
3E37c 8 3.57 20 0.20 0.89 182 0.29
3PE1d 68 30.79 75 0.75 0.97 1,744 0.71*
3PE1e 233 87.23 15 0.15 0.99 4,940 0.26
3PE2 263 1.15 4 0.04 0.94 65 0.54*
4ACM 19 29.87 55 0.55 0.97 1,559 0.57*
4BBGf 28 39.67 63 0.63 0.98 2,023 0.57*
4BBGg 31 48.39 59 0.59 0.99 2,467 0.46
4BBGh 13 40.38 83 0.83 0.98 2,059 0.75*
4PK5i 23 7.59 21 0.21 0.95 387 0.29
4PK5j 23 7.41 21 0.21 0.95 378 0.29

Notes:

a

3E37-I model is a four-point pharmacophore centered on two HBAs and two hydrophobic centers;

b

3E37-II model is a three-point pharmacophore centered on two HBAs and one hydrophobic center;

c

3E37-III model is a three-point pharmacophore centered on two HBAs and one hydrophobic center;

d

3PE1-I model is a six-point pharmacophore centered on one HBD, three HBAs, and two hydrophobic centers;

e

3PE1-II model is a four-point pharmacophore centered on one HBD, one HBA, and two hydrophobic centers;

f

4BBG-I model is a four-point pharmacophore centered on one positive ionizable group;

g

4BBG-II model is a four-point pharmacophore similar to the 4BBG-I model, except that an HBD replaces the positive ionizable group in the former model;

h

4BBG-III model is almost identical to 4BBG-I, but separated by exclusion volumes;

i

4PK5-I model is a three-point pharmacophore centered on one HBD and two hydrophobic centers; and

j

4PK5-II model is an almost identical model to 4PK5-I, but separated by exclusion volumes.

*

GH score >0.50.

Abbreviations: PDB, Protein Data Bank; TP, true positive; FP, false positive; TN, true negative; FN, false negative; EF, enrichment factor; GH, Güner–Henry; HBA, H-bond acceptor; HBD, H-bond donor.