. Author manuscript; available in PMC: 2014 Jul 7.

Published in final edited form as: Curr Top Med Chem. 2012;12(17):1869–1882. doi: 10.2174/156802612804547335

Table 2.

Performance comparison summary for the main model types on the targets described in this article.

NR	Compound discrimination problem			Pocket model performance^**	APF model
NR	actives	decoys	chem. difficulty^*	Pocket model performance^**	# seeds^***	performance^**
THRα	35	2280	1.62	91.96	4	100.00
THRβ	96	3618	0.38	95.74	9	99.62
RARα	27	1756	0.44	89.10	4	99.99
RARβ	47	1827	0.10	82.01	2	99.99
RARγ	42	1810	0.64	79.83	8	99.98
PPARα	85	3803	2.28	91.82	13	98.49
PPARδ	142	1261	9.46	82.80	18	98.56
PPARγ	207	3865	0.12	96.28	68	99.68
LXRβ	98	3968	3.98	87.06	7	99.70
LXRα	82	4072	12.26	90.64	7	97.76
FXR	23	1622	0.00	97.01	24	55.18
VDR	22	960	0.00	92.57	9	100.00
PXR	9	270	5.38	65.39	7	64.20
RXRα	80	1567	0.62	98.53	22	99.96
RXRβ	26	1096	21.42	99.91	2	99.89
ERα	384	4192	16.64	93.65	54	87.89
ERβ	349	4138	2.36	95.09	28	99.04
ERRα	17	1087	42.42	45.41	2	0.97
ERRγ	4	1198	0.00	100.00	8	100.00
GR	501	4597	19.20	54.23	7	70.52
MR	22	4669	27.90	76.20	6	86.68
PR	199	4713	36.88	58.08	14	91.82
AR	218	5858	5.14	84.41	23	95.61
STF1	6	409	62.56	84.44	4	99.92
LRH1	8	19	0.00	87.50	4	97.37
GPCR	Compound discrimination problem			Pocket model performance^**	APF model
GPCR	actives	decoys	chem. difficulty^*	Pocket model performance^**	# seeds^***	performance^**
CXCR4	51	896	100.00	60.92	2	78.24
OPRD	38	7761	37.53	58.69	1	89.59
OPRK	44	8997	35.94	38.22	1	73.02
OPRM	99	7192	60.85	51.93	1	83.43
OPRX	106	5857	100.00	45.40	1	72.78
A_A2AR	561	14293	16.48	82.77	6	91.89
ACM2	288	2548	47.86	47.75	1	79.26
ACM3	300	3541	34.75	56.10	1	89.95
β₁AR	50	1122	16.17	96.19	8	94.73
β₂AR	86	1597	13.01	91.74	7	88.01
DRD3	902	12795	88.69	59.22	1	65.49
HRH1	201	2469	86.27	78.28	1	78.36
S1PR1	85	1285	45.86	83.95	1	97.92

Chemical difficulty of the compound discrimination problem is evaluated as a normalized complement of ROC AUC for discrimination of actives against decoys by 2D chemical similarity to crystallographic seed ligands (see text for details).

^**

Model performance evaluated as the area under ROC curve for recognition of actives among property-matched decoys.

^***

Number of seeds reflects the amount of chemical information used in the model generation.