Open-source platform to benchmark fingerprints for ligand-based virtual screening

Riniker, Sereina; Landrum, Gregory A

doi:10.1186/1758-2946-5-26

Journal of Cheminformatics

Table 2 Information of data sets

From: Open-source platform to benchmark fingerprints for ligand-based virtual screening

Origin	Target ID	Description	A	D	A/D	BMS	B/A
MUV	466	Sphingosine 1-phosphate (S1P1) receptor	30	15000	0.002	30	1.00
	548	Protein kinase A (PKA)	30	15000	0.002	29	0.97
	600	Steroidogenic factor 1 (SF1): inhibitors	30	15000	0.002	29	0.97
	644	Rho-kinase 2	30	15000	0.002	28	0.93
	652	HIV-1 RT-Rnase H	30	15000	0.002	29	0.97
	689	Ephrin receptor A4	30	15000	0.002	30	1.00
	692	Steroidogenic factor 1 (SF1): agonists	30	15000	0.002	30	1.00
	712	Heat shock protein 90 (HSP90)	30	15000	0.002	27	0.90
	713	Estregon receptor (ER) α: inhibitors	30	15000	0.002	29	0.97
	733	Estregon receptor (ER) β	30	15000	0.002	30	1.00
	737	Estregon receptor (ER) α: potentiators	30	15000	0.002	29	0.97
	810	Focal adhesion kinase (FAK)	30	15000	0.002	28	0.93
	832	Cathepsin G	30	15000	0.002	25	0.83
	846	Factor XIa (FXIa)	30	15000	0.002	24	0.80
	852	Factor XIIa (FXIIa)	30	15000	0.002	24	0.80
	858	Dopamin receptor D1	30	15000	0.002	27	0.90
	859	Muscarinic receptor M1	30	15000	0.002	30	1.00
DUD	ace	Angiotensin-converting enzyme	46	1796	0.026	28	0.61
	ache	Acetylcholin esterase	99	3859	0.026	37	0.37
	ar	Androgen receptor	68	2848	0.024	21	0.31
	cdk2	Cyclin-dependent kinase 2	47	2070	0.023	39	0.83
	cox2	Cyclooxygenase-2	212	12606	0.011	97	0.46
	dhfr	Dihydrofolate reductase	190	8350	0.023	42	0.22
	egfr	Epidermal growth factor receptor	365	15560	0.023	86	0.24
	er_agonist	Estregon receptor (ER): agonists	63	2568	0.025	26	0.41
	fgfr1	Fibroblast growth factor receptor	71	3462	0.021	18	0.25
	fxa	Factor Xa	64	2092	0.031	28	0.44
	gpb	Glycogen phosphorylase	49¹	21321	0.023	14	0.29
	gr	Glucocorticoid receptor	32	2585	0.010	14	0.44
	hivrt	HIV-1 RT-Rnase	34	1494	0.023	25	0.74
	inha	Enoyl reductase	57	2707	0.021	35	0.61
	na	Neuramidase	49	1713	0.029	13	0.27
	p38	P38 MAP kinase	137	6779	0.020	47	0.34
	parp	Poly(ADP-ribose) polymerase	31	1350	0.023	9	0.29
	pdgfrb	Platelet-derived growth factor receptor β	124	5603	0.022	38	0.31
	sahh	S-adenosylhomocysteine hydrolase	33	1344²	0.025	10	0.30
	src	Tyrosine-protein kinase C-SRC	98	5679	0.011	30	0.31
	vegfr2	Vascular endothelial growth factor receptor 2	48	2712	0.011	39	0.81
ChEMBL	11359	Phosphodiesterase 4D	100	10000	0.010	81	0.81
	28	Thymidylate synthase	100	10000	0.010	48	0.48
	11536	Ghrelin receptor	100	10000	0.010	87	0.87
	8	Tyrosine-protein kinase ABL	100	10000	0.010	93	0.93
	10434	Tyrosine-protein kinase SRC	100	10000	0.010	94	0.94
	12670	Tyrosine-protein kinase receptor FLT3	100	10000	0.010	95	0.95
	20014	Serine/threonine-protein kinase Aurora-A	100	10000	0.010	87	0.87
	234	Insulin-like growth factor I receptor	100	10000	0.010	86	0.86
	12261	c-Jun N-terminal kinase I	100	10000	0.010	65	0.65
	12209	Carbonic anhydrase XII	100	10000	0.010	66	0.66
	25	Glucocorticoid receptor	100	10000	0.010	87	0.87
	36	Progesterone receptor	100	10000	0.010	78	0.78
	43	β-2 adrenergic receptor	100	10000	0.010	94	0.94
	219	Muscarinic acetylcholine receptor M3	100	10000	0.010	94	0.94
	130	Dopamine receptor D3	100	10000	0.010	92	0.92
	105	Serotonin 1d (5-HT1d) receptor	100	10000	0.010	66	0.66
	11336	Neuropeptide Y receptor type 5	100	10000	0.010	77	0.77
	20174	G protein-coupled receptor 44	100	10000	0.010	77	0.77
	126	Cyclooxygenase-2	100	10000	0.010	88	0.88
	11225	Renin	100	10000	0.010	81	0.81
	12252	β-secretase 1	100	10000	0.010	93	0.93
	11682	Glycine transporter 1	100	10000	0.010	76	0.76
	134	Vasopressin V1a receptor	100	10000	0.010	87	0.87
	116	Oxytocin receptor	100	10000	0.010	64	0.64
	11265	Somatostatin receptor 5	100	10000	0.010	59	0.59
	10475	Neuropeptide Y receptor type 1	100	10000	0.010	45	0.45
	12679	C5a anaphylatoxin chemotactic receptor	100	10000	0.010	45	0.45
	10579	C-C chemokine receptor type 4	100	10000	0.010	64	0.64
	11575	C-C chemokine receptor type 2	100	10000	0.010	80	0.80
	18061	Sodium channel protein type IX α subunit	100	10000	0.010	62	0.62
	237	Leukotriene A4 hydrolase	100	10000	0.010	65	0.65
	276	Phosphodiesterase 4A	100	10000	0.010	70	0.70
	11534	Cathepsin S	100	10000	0.010	91	0.91
	10198	Voltage-gated potassium channel subunit Kv1.5	100	10000	0.010	69	0.69
	10498	Cathepsin L	100	10000	0.010	90	0.90
	12911	Cytochrome P450 2C9	100	10000	0.010	96	0.96
	12968	Orexin receptor 2	100	10000	0.010	36	0.36
	100579	Nicotinic acid receptor 1	100	10000	0.010	70	0.70
	100126	Serine/threonine-protein kinase B-raf	100	10000	0.010	78	0.78
	10378	Cathepsin B	100	10000	0.010	83	0.83
	10417	P2X purinoceptor 7	100	10000	0.010	65	0.65
	10752	Inhibitor of nuclear factor κ B kinase β subunit	100	10000	0.010	64	0.64
	10773	Interleukin-8 receptor B	100	10000	0.010	55	0.55
	11631	Sphingosine 1-phosphate receptor Edg-1	100	10000	0.010	77	0.77
	10927	Urotensin II receptor	100	10000	0.010	59	0.59
	11085	Melatonin receptor 1B	100	10000	0.010	71	0.71
	11442	Liver glycogen phosphorylase	100	10000	0.010	55	0.55
	11279	Metabotropic glutamate receptor 1	100	10000	0.010	65	0.65
	11488	Estradiol 17- β-dehydrogenase 3	100	10000	0.010	47	0.47
	12840	Macrophage colony stimulating factor receptor	100	10000	0.010	81	0.81

List of 88 targets with data set origin, target ID, target description, number of actives (A), number of decoys (D), ratio actives/decoys (A/D), number of Bemis-Murcko scaffolds (BMS) found in the actives, and ratio BMS/actives (B/A).

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ISSN: 1758-2946

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