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

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.