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Protocols

DEKOIS specifications

Information


Unique identifier OMICS_33083
Name DEKOIS
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


No version available

Maintainer


  • person_outline Frank Boeckler

Publications for DEKOIS

DEKOIS citations

 (7)
call_split

Decoys Selection in Benchmarking Datasets: Overview and Perspectives

2018
Front Pharmacol
PMCID: 5787549
PMID: 29416509
DOI: 10.3389/fphar.2018.00011
call_split See protocol

[…] Among the recent tools to help create benchmarking sets (MUV, DEKOIS, DUD-E, and MUBD), the main difference resides in the strategy used to achieve their respective objectives: the DUD-E and DEKOIS data sets are designed for evaluating SBVS methods while MUV and […]

library_books

Rocker: Open source, easy to use tool for AUC and enrichment calculations and ROC visualization

2016
J Cheminform
PMCID: 5013620
PMID: 27606011
DOI: 10.1186/s13321-016-0158-y

[…] y is the appearance of databases of ligand binding data, e.g. ChEMBL [], and molecule collections, where not only active ligands but also decoy molecule sets are available, e.g. DUD [], DUD-e [], and DEKOIS [, ]. The other important issue in VS efficiency is the numerical and visual illustration of how well the VS method works. For this, two issues are typically calculated: (1) area under curve (A […]

call_split

1001 Ways to run AutoDock Vina for virtual screening

2016
J Comput Aided Mol Des
PMCID: 4801993
PMID: 26897747
DOI: 10.1007/s10822-016-9900-9
call_split See protocol

[…] he advantage of avoiding long drug development, making it possible to move quickly into more advanced phases of drug testing. Note that these libraries, however, differ from datasets like DUD-E [] or Dekois [], which are synthetic benchmarks suitable for evaluating the quality of docking algorithms. Benchmarking is not the goal of this study; the experiments here are aimed only at illustrating cha […]

library_books

Applying DEKOIS 2.0 in structure based virtual screening to probe the impact of preparation procedures and score normalization

2015
J Cheminform
PMCID: 4450982
PMID: 26034510
DOI: 10.1186/s13321-015-0074-6

[…] l findings observed for the bioactives.We recommend that computational/medicinal chemists should evaluate the available docking programs with several different preparation/docking setups – e.g. using DEKOIS 2.0 – to retrieve the best possible performance which then can be used for an actual SBVS effort. In addition, score normalization strategies eliminated the biased fitness shown by GOLD for the […]

library_books

Application of the 4D Fingerprint Method with a Robust Scoring Function for Scaffold Hopping and Drug Repurposing Strategies

2014
J Chem Inf Model
PMCID: 4210175
PMID: 25229183
DOI: 10.1021/ci5003872

[…] ng function and compared the current values to those obtained with the empirical HWZ scoring function using the multi conformational states of the decoys and active ligands of the 81 targets from the DEKOIS database. The merits of scoring function became clear as it accurately ranked compounds with subtle structural changes. In the present VS trial, we selected query molecules according to the pro […]

library_books

Performance Studies on Distributed Virtual Screening

2014
Biomed Res Int
PMCID: 4083208
PMID: 25032219
DOI: 10.1155/2014/624024

[…] fficient size to generate generalized benchmark data in terms of portal-based high-performance computing. In order to assess the influence of the target system itself, five smaller test sets from the DEKOIS [, ] test set were used (acetylcholine esterase, 1DX6; androgen receptor, 1E3G; estrogen receptor beta, 1I0G; HIV1 protease, 1HXW; and thrombin, 3RLW). Each set contains 40 active ligands and 1 […]

Citations

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DEKOIS institution(s)
Laboratory for Molecular Design and Pharmaceutical Biophysics, Department of Pharmaceutical and Medicinal Chemistry, Institute of Pharmacy, Eberhard Karls University Tuebingen, Tuebingen, Germany; Department of Pharmaceutical Chemistry, Faculty of Pharmacy and Biotechnology, German University in Cairo, Cairo, Egyp
DEKOIS funding source(s)
Supported by the GERLS (German-Egyptian Long-Term Scholarship) program of the German Academic Exchange Service (DAAD).

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