Computational Drug Discovery Software
Project description
www.opendiscovery.org.uk www.opendiscovery.co.uk
Version: 2.0.3
Contacts: gareth.price@warwick.ac.uk; a.marsh@warwick.ac.uk
Introduction
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.
Dependencies
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)
Terminology
Protocol Folder = the folder containing this readme, the odscreen.py and odparam.py files etc.
Ligand Folder = the folder with the config file, the folder with the ligands and the folder with the receptors in (PDB and PDBQT).
Tips (for the brave)
If you add alias odscreen="python /path/to/protocol_folder/odscreen.py " to your .bashrc or .bash_profile, or put the protocol folder in a folder already indexed by these files, you can call the script as:
odscreen -ARGS
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