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protein docking using a density-based descriptor for atoms charge and dynamics
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biobox Added stripped down biobox to be shipped with JabberDock Jul 3, 2019
methods updated Readme and corrected a typo in geometry Aug 13, 2019
.gitignore Added stripped down biobox to be shipped with JabberDock Jul 3, 2019
LICENSE updated Readme and corrected a typo in geometry Aug 13, 2019


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. -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


JabberDock requires python 2.7 and the following packages (and their associated packages):

  • numpy
  • biobox
  • cython
  • scipy
  • scikit-image
  • subprocess

JabberDock requires the following software to be installed to run:

  • gromacs 5.x
  • VMD 1.9.x
  • POWer

Install with: 'python install'

Biobox installation

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:


This is a work in progress, and there are bound to be issues/bugs. Please email the author at if you have any issues/bugs.

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