DecoyFinder has been updated to version 2.0. Decoy Finder is a graphical tool which helps finding sets of decoy molecules for a given group of active ligands. It does so 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. Optionally, a maximum Tanimoto value threshold can be set between decoys in order to assure chemical diversity in the decoy set.

There have been some changes in the dependencies, it now needs RDKit (with OpenBabel being optional) and PyQt4 instead of PySide.

Installation of RDKit was already described in the page on setting up a Mac for Cheminformatics, and I've now added the instructions for pyqt

brew install pyqt

cinfony is a common API to several cheminformatics toolkits. It uses the Python programming language, and builds on top of Open Babel, RDKit, the CDK, Indigo, JChem, OPSIN and cheminformatics webservices. Currently it is hosted on Googlecode which is closing down. Fortunately the source code is also hosted on github, but you will need to look at the Google code site to read full details of the project. So the installation is:-

git clone https://github.com/cinfony/cinfony.git
cd cinfony
python setup.py install

Then download the DecoyFinder2 source, and run

python decoy_finder.py