Skip to content
protein docking using a density-based descriptor for atoms charge and dynamics
Python Other
  1. Python 99.0%
  2. Other 1.0%
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
auto_scripts
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
README.md updated Readme and corrected a typo in geometry Aug 13, 2019
__init__.py
manual.pdf
setup.py

README.md

JabberDock

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

methods

  • 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):

  • 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 setup.py 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.

Usage

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

Contact

This is a work in progress, and there are bound to be issues/bugs. Please email the author at l.s.rudden@durham.ac.uk if you have any issues/bugs.

You can’t perform that action at this time.