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. 2016 Jul 4;10:2137–2154. doi: 10.2147/DDDT.S108118

Table 3.

Comparison of virtual screening results (number of compounds in hit list and hit rates) for the AfroCancer and NPACT datasets of the pharmacophore models generated

PDB code AfroCancer
NPACT
Number of hits Hit rate (%) Number of hits Hit rate (%)
1IEP 12 3.07* 11 0.70
2JDO 107 27.37* 338 21.47
2XMY 69 17.65* 223 14.17
3E37a 189 48.34 882 56.04
3E37b 228 58.31* 907 57.62
3E37c 95 24.30 440 27.95
3PE1d 37 9.46 149 9.47
3PE1e 3 0.77* 3 0.19
3PE2 106 27.11* 367 23.32
4ACM 35 8.95* 110 6.99
4BBGf 26 6.65a 93 5.91
4BBGg 0 0.00 0 0.00
4BBGh 1 0.26* 3 0.19
4PK5i 94 24.04* 301 19.12
4PK5j 102 26.09* 308 19.57

Notes:

*

Hit rate for AfroCancer supersedes that of NPACT;

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.

Abbreviations: NPACT, Naturally Occurring Plant-based Anticancer Compound-Activity-Target; PDB, Protein Data Bank; HBA, H-bond acceptor; HBD, H-bond donor.