DecoyFinder is a graphical tool which helps finding sets of decoy molecules for a given group of active ligands. It can do so by either finding molecules with a molecular weight similar to the actives (fast method) or by finding molecules which have a similar number of rotational bonds, hydrogen bond acceptors, hydrogen bond donors, logP value and molecular weight, but are chemically different, which is defined by a maximum Tanimoto value threshold between active ligand and decoy molecule MACCS fingerprints (slow method). Optionally, with this method a maximum Tanimoto value threshold can be set between decoys in order assure chemical diversity in the decoy set.
Adrià Cereto-Massagué (adrian.cereto at urv .cat), Laura Guasch, Miquel Mulero, Cristina Valls, Santiago García-Vallvé*, Gerard PujadasGrup de Recerca en Nutrigenòmica, Departament de Bioquímica i Biotecnologia, Universitat Rovira i Virgili, Campus de Sescelades, C/Marcel.lí Domingo s/n, 43007, Tarragona, Catalonia, Spain.
If you are running an OS for which there are no DecoyFinder packages available, you must make sure you have all the dependencies correctly installed and then it should work from the generic (source) package, just executing the following from a command line:
$ python PATH/TO/DECOYFINDER/decoy_finder.py
AGPLv3: GNU Affero General Public License version 3, wich can be read here
Adrià Cereto-Massagué (adrian.cereto at urv .cat)