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

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.