pROC-Chemotype Plot

Check out our protocol and paper on how to enhance the interpretability of benchmarking results in structure-based virtual screening with pROC-Chemotype Plots.

Please, do not forget to cite both our paper and the webpage when using or modifying the pROC-Chemotype Protocol.

The pROC-Chemotype Protocol: KNIME protocol and Pipeline Pilot protocol as published in:
pROC-Chemotype Plots Enhance the Interpretability of Benchmarking Results in Structure-Based Virtual Screening,
Ibrahim TM, Bauer MR, Dörr A, Veyisoglu E, Boeckler FM, JCIM 2015


DEKOIS 2.0: Demanding Evaluation Kits for Objective In silico Screening

This web page provides the DEKOIS 2.0 library of benchmark data sets previously described in 'Evaluation and Optimization of Virtual Screening Workflows with DEKOIS 2.0 – A Public Library of Challenging Docking Benchmark Sets' by Bauer MR, Ibrahim TM, Vogel SM, and Boeckler FM (JCIM 2013). All active and decoy data sets are prepared as sdf.gz files. Quality assessment metrics of the individual benchmark sets and a more in detail description of ligand set and decoys set generation protocol can be found in the DEKOIS 2.0 publication and the DEKOIS 2.0 supporting information. The complete DEKOIS 2.0 library can be downloaded here.


Active sets

Decoy sets

11-beta-Hydroxysteroid Dehydrogenase 1 
17-beta-Hydroxysteroid Dehydrogenase 1
Adenosine A2A receptor
Angiotensin-I-converting enzyme
Angiotensin-converting enzyme 2 
TNF Alpha Converting Enzyme
Beta-2 adrenergic receptor
RAC-alpha serine/threonine-protein kinase(PKB)
Aldose reductase
Androgen Receptor
Aurora A kinase
Aurora B kinase
Apoptosies Regulator B-cell lymphoma 2
Serine/threonine-protein kinase B-Raf
Cathepsin L
Cyclin-dependent kinase 2
Cathepsin K
Cytochrome P450 2A6
Dihydrofolate reductase
Epidermal growth factor receptor
Ephrin type-B receptor 4
Human Epidermal growth factor Receptor 2
Estrogen receptor beta
Fibroblast growth factor receptor 1
Peptidyl-prolyl cis-trans isomerase
Factor X (prothrombinase)
Glucocerebrosidase(Acid beta-Glucosidase)
Glucocorticoid receptor
Glycogen synthase kinase 3 beta
Histone Deacetylase 2
Histone Deacetylase 8
HIV-1 protease
HIV reverse transcriptase
HMG-CoA reductase
heat shock protein 90
Insulin-like growth factor I receptor
Enoyl ACP Reductase
IL2-inducible T-cell kinase
Janus Kinase 3
Mitogen-Activated Protein Kinase 8
Mitogen-activated protein kinase 9
Mitogen-Activated Protein Kinase 10
kinesin family member 11
Lymphocyte-specific protein tyrosine kinase
p53-Binding Protein MDM2
MAPK-activated Protein Kinase-2
Matrix Metalloproteinase-2
Neuraminidase A
P38 mitogen-activated protein kinases
PARP-1 (Poly [ADP-ribose] polymerase 1
Phosphodiesterase Type 4
cGMP-specific phosphodiesterase type 5
Pyruvate dehydrogenase kinase, isozyme 1
Phosphoinositid-3-Kinase gamma
Serine/threonine-protein kinase pim-1
Serine/threonine-protein kinase pim-2
Purine nucleoside phosphorylase
Peroxisome proliferator-activated receptor alpha
Peroxisome proliferator-activated receptor gamma
Progesterone Receptor
Protein Kinase C theta
Glycogenphosphorylase (inner dimer site)
Glycogenphosphorylase (outer dimer site)
Glutaminyl-peptide cyclotransferase
Rho-associated protein kinase-1
Retinoid X receptor alpha
SARS Coronavirus 3C-like Protease
NAD-Dependent Deacetylase Sirtuin-2
Proto-oncogene tyrosine-protein kinase Src
Angiopoietin-1 receptor
Thymidine kinase
Thymidine Phosphorylase
Tissue plasminogen activator
Thymidylate Synthase
Urokinase Plasminogen activator
Vascular endothelial growth factor rec. 1
Vascular endothelial growth factor rec. 2

Here you can access the original DEKOIS sets as published in:
Vogel SM, Bauer MR, Boeckler FM, JCIM 2011