DecoyFinder

A Tool for finding decoy molecule sets for given active ligand sets

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.

Index

Authors
Downloads
Install
Dependencies
Documentation
License
Contact

Authors

Adrià Cereto-Massagué (adrian.cereto at urv .cat), Laura Guasch, Miquel Mulero, Cristina Valls, Santiago García-Vallvé*, Gerard Pujadas

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, Catalonia, Spain.
Centre Tecnològic de Nutrició i Salut (CTNS), TECNIO, CEICS, Camí de Valls, 81-87, 43204 Reus, Catalonia, Spain

If you use DecoyFinder for your research, please cite the following article:

Cereto-Massague, A., Guasch, L., Valls, C., Mulero, M., Pujadas, G., & Garcia-Vallve, S. (2012). DecoyFinder: an easy-to-use python GUI application for building target-specific decoy sets. Bioinformatics, 2-3. doi:10.1093/bioinformatics/bts249

Downloads

Source

Install

Windows users: just use the installer, all needed files are provided.
Ubuntu 12.04 LTS and Debian users: simply install the provided .deb package, all dependencies will be automatically installed by the package manager. If you open the .deb package using the software center, it may complain about the package being of bad quality and advice against its installation. Just ignore the warning. This will be fixed in future releases.
Other Linux users: the 32-bit static standalone executable should work on any system with GLIBC >= 2.15

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

Dependencies

Python >= 2.5, < 3
RDKit
OpenBabel (optional; for extra supported file formats)
Cinfony
PyQt4 >= 4.6

Documentation

Documentation is available here

License

AGPLv3: GNU Affero General Public License version 3, wich can be read here

Contact

Adrià Cereto-Massagué (adrian.cereto at urv .cat)