JabberDock provides a mechanism to dock two protein STID maps together in conjunction with the POW engine and BioBox
Note that it requires BioBOx as a means to generate the STID maps, and POW to run the optimisation.
This version of JabberDock ships with a version of biobox intended to allow it to work.
auto_scripts Command line features are provided in the auto_scripts folder.
- Help for each one for be provided by typing the command follows by -h, e.g. dock.py -h
- The commands should be accessible in your PYTHONPATH
- More information on each command is provided in the accompanying manual
- In here you will find all the python scripts called by the various commands in auto_scripts
- Each one has documentation written out, this can be read either directly in the file, or via the manual
- There are a few additional commands provided for users which are not used by the commands in auto_scripts...
- For example, the create_pqr_dat in data, which can convert an rtp file into a readable dat pqr file to create STID maps
INSTALLATION AND REQUIREMENTS
JabberDock requires python 2.7 and the following packages (and their associated packages):
JabberDock requires the following software to be installed to run:
- gromacs 5.x
- VMD 1.9.x
Install with: 'python setup.py install'
Shipped with this version of JabberDock is a heavily stripped version of biobox containing the functions JabberDock requires. Please move the biobox folder into whatever directory you like (e.g. your home), just make sure it's in your pythonpath There is a readme file in the biobox folder containing instructions on requirements and installation instructions.
Please see the manual in the home directory for more details on how to use JabberDock. Please email the author if you have any issues / bugs.
When using JabberDock in your work, please cite the following publication: https://pubs.acs.org/doi/10.1021/acs.jctc.9b00474
This is a work in progress, and there are bound to be issues/bugs. Please email the author at email@example.com if you have any issues/bugs.