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