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) | Description | Ligands | Difficulty | |
1 | PPARD | 2J14 | -0.10 | 3DY6 | 0.51 | Peroxisome proliferator-activated receptor delta | 21 | Very Hard |
2 | KIF11 | 2UYI | -0.06 | 2UYM | 0.11 | Kinesin-like protein 1 | 32 | Very Hard |
3 | HDAC8 | 3SFH | -1.00 | 3SFF | 1.00 | Histone deacetylase 8 | 7 | Very Hard |
4 | ROCK1 | 3V8S | -0.50 | 2ESM | 0.92 | Rho-associated protein kinase 1 | 12 | Very Hard |
5 | WEE1 | 3BIZ | -0.60 | 1X8B | 0.80 | Serine/threonine-protein kinase WEE1 | 8 | Very Hard |
6 | FPPS | 3RYE | -0.11 | 4JVJ | 0.86 | Farnesyl diphosphate synthase | 30 | Very Hard |
7 | ITAL | 1XDG | 0.46 | 1XUO | 0.37 | Leukocyte adhesion glycoprotein LFA-1 alpha | 13 | Medium |
8 | JAK2 | 4GFM | 0.26 | 4AQC | 0.20 | Tyrosine-protein kinase JAK2 | 48 | Medium |
9 | FAK1 | 4GU9 | 0.34 | 4K9Y | 0.22 | Focal adhesion kinase 1 | 21 | Medium |
10 | PPARG | 1RDT | 0.35 | 3U9Q | 0.17 | Peroxisome proliferator-activated receptor gamma | 116 | Medium |
11 | CSF1R | 3DPK | 0.49 | 2I0V | 0.10 | Macrophage colony stimulating factor receptor | 12 | Medium |
12 | PTN1 | 3EAX | 0.42 | 1LQF | 0.08 | Protein-tyrosine phosphatase 1B | 74 | Medium |
13 | TRY1 | 2AH4 | 0.43 | 1GBT | 0.92 | Trypsin I | 169 | Medium |
14 | HS90A | 2BT0 | 0.47 | 4EGI | 0.75 | Heat shock protein HSP 90-alpha | 175 | Medium |
15 | ESR1 | 2P15 | 0.34 | 1YIM | 0.36 | Estrogen receptor alpha | 104 | Medium |
16 | BRAF | 4H58 | 0.39 | 3IDP | 0.30 | Serine/threonine-protein kinase B-raf | 46 | Medium |
17 | ABL1 | 2F4J | 0.48 | 2HZ0 | 0.33 | Tyrosine-protein kinase ABL | 39 | Medium |
18 | SRC | 3UQG | 0.27 | 4FIC | 0.27 | Tyrosine-protein kinase SRC | 48 | Medium |
19 | ACES | 1QTI | 0.47 | 1GQS | 0.38 | Acetylcholinesterase | 41 | Medium |
20 | HMDH | 2Q6B | 0.44 | 2Q6B | 0.16 | HMG-CoA reductase | 19 | Medium |
21 | MET | 3LQ8 | 0.44 | 3RHK | 0.17 | Hepatocyte growth factor receptor | 49 | Medium |
22 | MCR | 3WFF | 0.40 | 1YA3 | 0.33 | Mineralocorticoid receptor | 18 | Medium |
23 | XIAP | 4HY0 | 0.40 | 2OPY | 0.63 | Inhibitor of apoptosis protein 3 | 21 | Medium |
24 | MAPK2 | 3FPM | 0.00 | 2P3G | 0.59 | MAP kinase-activated protein kinase 2 | 13 | Hard |
25 | MK14 | 1WBW | 0.13 | 4LOO | 0.05 | MAP kinase p38 alpha | 176 | Hard |
26 | HIVRT | 1S1U | 0.22 | 3LP2 | 0.05 | Human immunodeficiency virus type 1 reverse transcriptase | 169 | Hard |
27 | THRB | 2ZFF | 0.21 | 4BAO | 0.12 | Thrombin | 216 | Hard |
28 | EGFR | 3W2Q | 0.24 | 2ITT | 0.41 | Epidermal growth factor receptor erbB1 | 81 | Hard |
29 | GRIA2 | 1MQH | 0.10 | 3T9V | 0.22 | Glutamate receptor ionotropic AMPA 2 | 84 | Hard |
30 | LKHA4 | 3B7R | 0.00 | 3FUF | 0.17 | Leukotriene A4 hydrolase | 39 | Hard |
31 | MK10 | 2O0U | 0.03 | 1PMU | 0.10 | c-Jun N-terminal kinase 3 | 59 | Hard |
32 | DPP4 | 3CCC | 0.18 | 3CCC | 0.07 | Dipeptidyl peptidase IV | 71 | Hard |
33 | RENI | 2G1S | 0.12 | 4GJ9 | 0.12 | Renin | 46 | Hard |
34 | PPARA | 3G8I | 0.10 | 3KDU | 0.86 | Peroxisome proliferator-activated receptor alpha | 15 | Hard |
35 | ESR2 | 1NDE | 0.19 | 1QKN | 0.15 | Estrogen receptor beta | 32 | Hard |
36 | IGF1R | 3O23 | 0.18 | 3O23 | 0.18 | Insulin-like growth factor I receptor | 13 | Hard |
37 | CAH2 | 1BCD | 0.14 | 3M2Y | 0.15 | Carbonic anhydrase II | 242 | Hard |
38 | MMP13 | 2PJT | 0.14 | 2PJT | 0.08 | Matrix metalloproteinase 13 | 28 | Hard |
39 | ANDR | 2YLQ | 0.89 | 2HVC | 0.49 | Androgen Receptor | 92 | Easy |
40 | CASP3 | 1RHU | 1.00 | 2CNK | 0.94 | Caspase-3 | 21 | Easy |
41 | FA10 | 2XBV | 0.97 | 2Y7Z | 0.29 | Coagulation factor X | 104 | Easy |
42 | FA7 | 1W7X | 0.73 | 1W7X | 0.63 | Coagulation factor VII | 42 | Easy |
43 | AKT1 | 3CQW | 0.64 | 3OCB | 0.78 | Serine/threonine-protein kinase AKT | 11 | Easy |
44 | PARP1 | 4HHZ | 0.70 | 1UK0 | 0.34 | Poly [ADP-ribose] polymerase-1 | 17 | Easy |
45 | TGFR1 | 3HMM | 0.86 | 3HMM | 0.90 | TGF-beta receptor type I | 15 | Easy |
46 | PDE5A | 3TGG | 0.69 | 3SIE | 0.08 | Phosphodiesterase 5A | 26 | Easy |
47 | FABP4 | 3P6G | 0.90 | 1LID | 0.91 | Fatty acid binding protein adipocyte | 22 | Easy |
48 | LCK | 2OG8 | 0.51 | 2OG8 | 0.15 | Tyrosine-protein kinase LCK | 32 | Easy |
49 | PLK1 | 4A4L | 0.57 | 2OU7 | 0.30 | Serine/threonine-protein kinase PLK1 | 10 | Easy |
50 | VGFR2 | 4AG8 | 0.63 | 3CPB | 0.29 | Vascular endothelial growth factor receptor 2 | 24 | Easy |
51 | HDAC2 | 4LY1 | 1.00 | 4LY1 | 1.00 | Histone deacetylase 2 | 3 | Easy |
52 | AKT2 | 3D0E | 1.00 | 2XH5 | 1.00 | Serine/threonine-protein kinase AKT2 | 10 | Easy |
53 | ADA17 | 3LGP | 0.80 | 3LGP | 0.49 | ADAM17 | 12 | Easy |
54 | PYGM | 2G9R | 1.00 | 2G9R | 1.00 | Muscle glycogen phosphorylase | 18 | Easy |
55 | DEF | 2AI8 | 1.00 | 2AI8 | 1.00 | Peptide deformylase | 10 | Easy |
56 | PGH2 | 4OTY | 1.00 | 3OLT | 1.00 | Cyclooxygenase-2 | 30 | Easy |
57 | PA2GA | 1DCY | 0.50 | 1DB5 | 0.97 | Phospholipase A2 group IIA | 8 | Easy |
58 | NRAM | 1B9S | 0.83 | 1VCJ | 0.70 | Neuraminidase | 12 | Easy |
59 | FKB1A | 2FAP | 1.00 | 2FKE | 1.00 | FK506-binding protein 1A | 26 | Easy |
60 | PRGR | 4A2J | 0.80 | 2OVH | 0.29 | Progesterone receptor | 18 | Easy |
61 | FNTA | 1QBQ | 1.00 | 3KSL | 1.00 | Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit | 23 | Easy |
62 | GLCM | 2XWE | 1.00 | 3RIL | 1.00 | Beta-glucocerebrosidase | 9 | Easy |
63 | RXRA | 3OZJ | 1.00 | 4K4J | 1.00 | Retinoid X receptor alpha | 42 | Easy |
64 | THB | 2PIN | 1.00 | 2PIN | 1.00 | Thyroid hormone receptor beta-1 | 14 | Easy |
65 | MP2K1 | 3ZLW | 0.50 | 4ARK | 0.74 | Dual specificity mitogen-activated protein kinase kinase 1 | 8 | Easy |
66 | MK01 | 4GT3 | 1.00 | 3SA0 | 0.99 | MAP kinase ERK2 | 69 | Easy |
67 | KIT | 4HVS | 1.00 | 4HVS | 1.00 | Stem cell growth factor receptor | 6 | Easy |
68 | HIVIN | 3NF9 | 1.00 | 3NF9 | 1.00 | Human immunodeficiency virus type 1 integrase | 8 | Easy |
69 | HIVPR | 1HVS | 0.62 | 301 | ||||
70 | CDK2 | 2VTH | 0.57 | 39 | ||||
71 | BACE1 | 2B8L | 0.51 | 56 |
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.
Scripts and website content © 2024 Shayne Wierbowski - University of Scranton. Website content © 2024 Jim Zheng - University of Pittsburgh. All rights reserved.