Ranking - Cross Docking Benchmark

Benchmark Targets

The default benchmark contains 95 targets selected from the DUD-E Targets list. The targets are presented and described here. You may generate your own benchmark or specialized crossdocking dataset using the Generate tab. Please reference DUD-E for more information regarding the targets. Specifically, see the DUDE wiki page for documentation and discussion.

#	Target	Receptor (SPM)	SPM	Receptor (R2)	R2	Description	Ligands	Difficulty
1	ABL1	2F4J	0.48	2HZ0	0.33	Tyrosine-protein kinase ABL	39	Medium
2	ACES	1QTI	0.47	1GQS	0.38	Acetylcholinesterase	41	Medium
3	ADA17	3LGP	0.80	3LGP	0.49	ADAM17	12	Easy
4	AKT1	3CQW	0.64	3OCB	0.78	Serine/threonine-protein kinase AKT	11	Easy
5	AKT2	3D0E	1.00	2XH5	1.00	Serine/threonine-protein kinase AKT2	10	Easy
6	ANDR	2YLQ	0.89	2HVC	0.49	Androgen Receptor	92	Easy
7	BACE1	2B8L	0.51				56
8	BRAF	4H58	0.39	3IDP	0.30	Serine/threonine-protein kinase B-raf	46	Medium
9	CAH2	1BCD	0.14	3M2Y	0.15	Carbonic anhydrase II	242	Hard
10	CASP3	1RHU	1.00	2CNK	0.94	Caspase-3	21	Easy
11	CDK2	2VTH	0.57				39
12	CSF1R	3DPK	0.49	2I0V	0.10	Macrophage colony stimulating factor receptor	12	Medium
13	DEF	2AI8	1.00	2AI8	1.00	Peptide deformylase	10	Easy
14	DPP4	3CCC	0.18	3CCC	0.07	Dipeptidyl peptidase IV	71	Hard
15	EGFR	3W2Q	0.24	2ITT	0.41	Epidermal growth factor receptor erbB1	81	Hard
16	ESR1	2P15	0.34	1YIM	0.36	Estrogen receptor alpha	104	Medium
17	ESR2	1NDE	0.19	1QKN	0.15	Estrogen receptor beta	32	Hard
18	FA10	2XBV	0.97	2Y7Z	0.29	Coagulation factor X	104	Easy
19	FA7	1W7X	0.73	1W7X	0.63	Coagulation factor VII	42	Easy
20	FABP4	3P6G	0.90	1LID	0.91	Fatty acid binding protein adipocyte	22	Easy
21	FAK1	4GU9	0.34	4K9Y	0.22	Focal adhesion kinase 1	21	Medium
22	FKB1A	2FAP	1.00	2FKE	1.00	FK506-binding protein 1A	26	Easy
23	FNTA	1QBQ	1.00	3KSL	1.00	Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit	23	Easy
24	FPPS	3RYE	-0.11	4JVJ	0.86	Farnesyl diphosphate synthase	30	Very Hard
25	GLCM	2XWE	1.00	3RIL	1.00	Beta-glucocerebrosidase	9	Easy
26	GRIA2	1MQH	0.10	3T9V	0.22	Glutamate receptor ionotropic AMPA 2	84	Hard
27	HDAC2	4LY1	1.00	4LY1	1.00	Histone deacetylase 2	3	Easy
28	HDAC8	3SFH	-1.00	3SFF	1.00	Histone deacetylase 8	7	Very Hard
29	HIVIN	3NF9	1.00	3NF9	1.00	Human immunodeficiency virus type 1 integrase	8	Easy
30	HIVPR	1HVS	0.62				301
31	HIVRT	1S1U	0.22	3LP2	0.05	Human immunodeficiency virus type 1 reverse transcriptase	169	Hard
32	HMDH	2Q6B	0.44	2Q6B	0.16	HMG-CoA reductase	19	Medium
33	HS90A	2BT0	0.47	4EGI	0.75	Heat shock protein HSP 90-alpha	175	Medium
34	IGF1R	3O23	0.18	3O23	0.18	Insulin-like growth factor I receptor	13	Hard
35	ITAL	1XDG	0.46	1XUO	0.37	Leukocyte adhesion glycoprotein LFA-1 alpha	13	Medium
36	JAK2	4GFM	0.26	4AQC	0.20	Tyrosine-protein kinase JAK2	48	Medium
37	KIF11	2UYI	-0.06	2UYM	0.11	Kinesin-like protein 1	32	Very Hard
38	KIT	4HVS	1.00	4HVS	1.00	Stem cell growth factor receptor	6	Easy
39	LCK	2OG8	0.51	2OG8	0.15	Tyrosine-protein kinase LCK	32	Easy
40	LKHA4	3B7R	0.00	3FUF	0.17	Leukotriene A4 hydrolase	39	Hard
41	MAPK2	3FPM	0.00	2P3G	0.59	MAP kinase-activated protein kinase 2	13	Hard
42	MCR	3WFF	0.40	1YA3	0.33	Mineralocorticoid receptor	18	Medium
43	MET	3LQ8	0.44	3RHK	0.17	Hepatocyte growth factor receptor	49	Medium
44	MK01	4GT3	1.00	3SA0	0.99	MAP kinase ERK2	69	Easy
45	MK10	2O0U	0.03	1PMU	0.10	c-Jun N-terminal kinase 3	59	Hard
46	MK14	1WBW	0.13	4LOO	0.05	MAP kinase p38 alpha	176	Hard
47	MMP13	2PJT	0.14	2PJT	0.08	Matrix metalloproteinase 13	28	Hard
48	MP2K1	3ZLW	0.50	4ARK	0.74	Dual specificity mitogen-activated protein kinase kinase 1	8	Easy
49	NRAM	1B9S	0.83	1VCJ	0.70	Neuraminidase	12	Easy
50	PA2GA	1DCY	0.50	1DB5	0.97	Phospholipase A2 group IIA	8	Easy
51	PARP1	4HHZ	0.70	1UK0	0.34	Poly [ADP-ribose] polymerase-1	17	Easy
52	PDE5A	3TGG	0.69	3SIE	0.08	Phosphodiesterase 5A	26	Easy
53	PGH2	4OTY	1.00	3OLT	1.00	Cyclooxygenase-2	30	Easy
54	PLK1	4A4L	0.57	2OU7	0.30	Serine/threonine-protein kinase PLK1	10	Easy
55	PPARA	3G8I	0.10	3KDU	0.86	Peroxisome proliferator-activated receptor alpha	15	Hard
56	PPARD	2J14	-0.10	3DY6	0.51	Peroxisome proliferator-activated receptor delta	21	Very Hard
57	PPARG	1RDT	0.35	3U9Q	0.17	Peroxisome proliferator-activated receptor gamma	116	Medium
58	PRGR	4A2J	0.80	2OVH	0.29	Progesterone receptor	18	Easy
59	PTN1	3EAX	0.42	1LQF	0.08	Protein-tyrosine phosphatase 1B	74	Medium
60	PYGM	2G9R	1.00	2G9R	1.00	Muscle glycogen phosphorylase	18	Easy
61	RENI	2G1S	0.12	4GJ9	0.12	Renin	46	Hard
62	ROCK1	3V8S	-0.50	2ESM	0.92	Rho-associated protein kinase 1	12	Very Hard
63	RXRA	3OZJ	1.00	4K4J	1.00	Retinoid X receptor alpha	42	Easy
64	SRC	3UQG	0.27	4FIC	0.27	Tyrosine-protein kinase SRC	48	Medium
65	TGFR1	3HMM	0.86	3HMM	0.90	TGF-beta receptor type I	15	Easy
66	THB	2PIN	1.00	2PIN	1.00	Thyroid hormone receptor beta-1	14	Easy
67	THRB	2ZFF	0.21	4BAO	0.12	Thrombin	216	Hard
68	TRY1	2AH4	0.43	1GBT	0.92	Trypsin I	169	Medium
69	VGFR2	4AG8	0.63	3CPB	0.29	Vascular endothelial growth factor receptor 2	24	Easy
70	WEE1	3BIZ	-0.60	1X8B	0.80	Serine/threonine-protein kinase WEE1	8	Very Hard
71	XIAP	4HY0	0.40	2OPY	0.63	Inhibitor of apoptosis protein 3	21	Medium

Cross Docking Benchmark is provided by the Camacho Laboratory at University of Pittsburgh and is developed by Shayne Wierbowski of the University of Scranton and Jim Zheng of the University of Pittsburgh.