GenDock

GenDock is a Python script that will generate molecules to dock against a receptor using a combination of autodock-vina and machine learning to improve the speed of ligand identification

Setup

GenDock requires a few other modules. Create a virtualenv that contains rdkit tensorflow numpy autodock-vina

git clone https://github.com/philspence/gendock.git
cd gendock
mkdir receptors
cp path/to/receptor.pdbqt receptors/receptor.pdbqt

Running GenDock

Arguments:
-r receptor name (no extension)
-c centre of the search grid that vina will use
-s size of the search grid that vina will use

python gendock.py -r receptor -c 0 0 0 -s 20 20 20

Results

GenDock will save a CSV file in the data directory that will contain the SMILES string of the ligand, the name of the receptor, the binding energy calculated from vina and the predicted energy (0 for those that aren't predicted).

References

AutoDock Vina: J Comput Chem. 2010 Jan 30;31(2):455-61. doi:10.1002/jcc.21334

OpenBabel: J. Cheminf. 2011, 3, 33. doi:10.1186/1758-2946-3-33

RDKit: Cheminformatics and Machine Learning Software. RDKit.org