. Author manuscript; available in PMC: 2016 Feb 23.

Published in final edited form as: J Chem Inf Model. 2015 Feb 6;55(2):407–420. doi: 10.1021/ci500691p

Table 4.

Comparison of enrichments for different docking and pharmacophore modeling methods.

Targets	Methods	EF₁	EF₁₀	EF₂₀	AUC
HIVPR	4F SILCS-Pharm^a	6.7	4.1	3.6	0.78
	5F Modified SILCS-Pharm^b	77.1	9.2	4.4	0.89
	Original SILCS-Pharm^c	99.6	9.8	4.3	0.88
	DOCK 4.0	2.0	1.5	1.2	0.58
	AutoDock 4	0	2.1	1.5	0.56
	AutoDock Vina	4.2	3.6	2.8	0.73
	FPP^d	9.3	4.7	3.5	0.81
	HSRP^d	-	-	-	<0.80^e

FXa	4F SILCS-Pharm^a	41.9	11.4	5.1	0.91
	Original SILCS-Pharm^c	20.7	6.5	3.5	0.81
	DOCK 4.0	26.3	4.2	2.6	0.76
	AutoDock 4	0.7	0.7	0.7	0.42
	AutoDock Vina	3.8	1.5	1.6	0.64
	FPP^d	12.2–29.7	5.6–6.7	3.5–3.9	0.81–0.87^f
	HSRP^d	-	-	-	<0.83^e

DHFR	3F SILCS-Pharm^a	29.3	4.8	3.0	0.79
	Original SILCS-Pharm^c	0.0	5.5	4.0	0.87
	DOCK 4.0	6.3	1.8	1.8	0.66
	AutoDock 4	6.3	2.8	2.8	0.76
	AutoDock Vina	3.8	1.7	1.2	0.65
	FFP^d	2.0	1.5	1.3	0.51
	HSRP^d	-	-	-	<0.62^e

FGFr1	3F SILCS-Pharm^a	0.8	1.5	0.8	0.55
	DOCK 4.0	1.7	0.8	0.7	0.33
	AutoDock 4	0.0	0.6	0.4	0.38
	AutoDock Vina	0.0	1.2	1.2	0.50

P38 MAP	3F SILCS-Pharm^a	6.4	1.8	1.3	0.57
	DOCK 4.0	2.0	1.1	0.7	0.39
	AutoDock 4	2.0	0.7	0.8	0.45
	AutoDock Vina	2.5	2.4	1.8	0.59

ADA	3F SILCS-Pharm^a	0.0	3.8	3.0	0.80
	DOCK 4.0	0.0	4.3	2.7	0.79
	AutoDock 4	0.0	1.8	1.3	0.46
	AutoDock Vina	0.0	0.0	0.0	0.36

ER_antagonist	4F SILCS-Pharm^a	14.3	10.3	4.6	0.81
	DOCK 4.0	0.0	0.8	0.8	0.46
	AutoDock 4	6.0	4.2	2.5	0.64
	AutoDock Vina	2.8	2.4	1.7	0.59

AmpC	3F SILCS-Pharm^a	5.0	2.0	3.6	0.70
	DOCK 4.0	104.6	9.5	4.7	0.87
	AutoDock 4	0.0	1.0	1.4	0.58
	AutoDock Vina	0.0	0.0	0.5	0.35

The results of the best performing SILCS pharmacophore model based on AUC with a specific number of key features (e.g. 4F means 4 top FGFE ranked features are considered as key features in the model) are shown.

The best modified model for HIVPR with the POS feature changed into a HBDON|POS feature.

The best results from the original SILCS-Pharm work¹⁶.

Full Protein Pharmacophore (FPP) and Hydration Site Restricted Pharmacophore (HSRP) results from Lill and coworkers work⁷.

The upper AUC values for HSRP models using different parameters are estimated from figure 7 in Ref.⁷ as no exact values were reported.

Three protein structures were used for FXa in Ref.⁷, so the range of AUC values is shown here.