General Information
| Description | An easy-to-use python GUI application for building target-specific decoy sets |
| Homepage | http://URVnutrigenomica-CTNS.github.com/DecoyFinder |
Publications
DecoyFinder: an easy-to-use python GUI application for building target-specific decoy sets
Summary:
Decoys are molecules that are presumed to be inactive against a target (i.e. will not likely bind to the target) and are used to validate the performance of molecular docking or a virtual screening workflow. The Directory of Useful Decoys database (http://dud.docking.org/) provides a free directory of decoys for use in virtual screening, though it only contains a limited set of decoys for 40 targets.To overcome this limitation, we have developed an application called DecoyFinder that selects, for a given collection of active ligands of a target, a set of decoys from a database of compounds. Decoys are selected if they are similar to active ligands according to five physical descriptors (molecular weight, number of rotational bonds, total hydrogen bond donors, total hydrogen bond acceptors and the octanol–water partition coefficient) without being chemically similar to any of the active ligands used as an input (according to the Tanimoto coefficient between MACCS fingerprints). To the best of our knowledge, DecoyFinder is the first application designed to build target-specific decoy sets.
Availability:
A complete description of the software is included on the application home page. A validation of DecoyFinder on 10 DUD targets is provided as Supplementary Table S1. DecoyFinder is freely available at http://URVnutrigenomica-CTNS.github.com/DecoyFinder
Contact:
santi.garcia-vallve@urv.cat
Supplementary information:
Supplementary data are available at Bioinformatics online.
Related Tools
VSDocker
Published April 2010
A tool for parallel high-throughput virtual screening using AutoDock on Windows-based computer clusters
TarPred
Published February 2015
A web application for predicting therapeutic and side effect targets of chemical compounds
LIGSIFT
Published October 2014
An open-source tool for ligand structural alignment and virtual screening
3DRobot
Published October 2015
Automated generation of diverse and well-packed protein structure decoys
RADER
Published January 2017
A RApid DEcoy Retriever to facilitate decoy based assessment of virtual screening
FAIR Evaluation
Sorry, you must be signed in to evaluate this object.
