Computational Drug Discovery Software
Open Discovery is a suite of programs that use Open Source or freely available tools to dock a library of chemical compounds against a receptor protein. In a (currently submitted) paper in the Journal of Chemical Education, we outline the usefulness of having an uncomplicated, free-to-use protocol to accomplish a task that has been the subject of academic and commercial interest for decades. We also highlight the gaps in open source tools around preparing protein - ligand complexes for molecular simulation, an area we expect to develop in the future.
- Python (you probably have this, install from http://www.python.org/getit/ - version developed with: 2.7)
- Open Babel (install from http://openbabel.org/ - version developed with: 2.3.1)
- AutoDock Vina binary (provided in lib folder, but downloaded from http://vina.scripps.edu - version developed with: 1.1.2)
- Protocol Folder = the folder containing this readme and odscreen.py
- Ligand Folder = the folder with the config file, the folder with the ligands and the folder with the receptors in (PDB and PDBQT).
A simple walkthrough for this new version will be created shortly. The original version can be found here