title: DecoyFinder: an easy-to-use python GUI application for building target-specific decoy sets.
abstract: 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.
  
  
  BACKGROUND
  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.
authors.affiliation: Grup de Recerca en Nutrigenòmica, Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Campus de Sescelades, C/Marcel.lí Domingo s/n, 43007 Tarragona, Spain.
authors.forename: Adrià
authors.initials: A
authors.lastname: Cereto-Massagué
authors.forename: Laura
authors.initials: L
authors.lastname: Guasch
authors.forename: Cristina
authors.initials: C
authors.lastname: Valls
authors.forename: Miquel
authors.initials: M
authors.lastname: Mulero
authors.forename: Gerard
authors.initials: G
authors.lastname: Pujadas
authors.forename: Santiago
authors.initials: S
authors.lastname: Garcia-Vallvé
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D003196:Computer Graphics; D016208:Databases, Factual; D006860:Hydrogen Bonding; D008024:Ligands; D008958:Models, Molecular; D008970:Molecular Weight; D011506:Proteins / Q000032:analysis*; D012984:Software; D014584:User-Computer Interface
chemical_list: D008024:Ligands; D011506:Proteins