Citation:
https://springerplus.springeropen.com/articles/10.1186/s40064-016-1972-4
Shamsara, J. (2016). "CrossDocker: a tool for performing cross-docking using Autodock Vina." SpringerPlus 5(1): 1.
@article{shamsara2016crossdocker,
author = {Shamsara, Jamal},
title = {{CrossDocker}: a tool for performing cross-docking using {Autodock Vina}},
journal = {SpringerPlus},
year = {2016},
volume = {5},
pages = {1},
doi = {10.1186/s40064-016-1972-4}
}Download:
The executable, bundled Vina binary, sample datasets, and standalone source
bundle are attached to the v1.0 release
rather than committed in this repository (they're binaries/archives, so
Releases is a better fit than the git tree). The source/ folder here has
the plain Python source for reference/review.
Installing:
The executable was built for windows. There is no need to installation; just extract contents of the CrossDocker.zip archieve in desired directory.
Prerequisites:
Open Babel 2.3 or higher is needed for successful execution of CrossDocker.
By default babel.exe is expected on the PATH environment variable; if it is
not, add it before running CrossDocker.
MGLTools / AutoDockTools must also be installed. CrossDocker does not bundle
it: source/adt_ligand_prep.py and source/adt_receptor_prep.py are thin
adapters that import MolKit and AutoDockTools from your own MGLTools
installation. Download it from http://mgltools.scripps.edu and make sure its
Python packages are importable by the interpreter running CrossDocker.
Usage:
Set the parameters defined in the config.txt file. Run the CrossDocker.exe file from command line. To test the CrossDocker the small_dataset can be used.
Tip: set_vina_priority_high.bat / set_vina_priority_low.bat set the
running vina.exe process to high or idle CPU priority (via wmic ... setpriority), if you want docking to run faster or stay in the background
without slowing down other programs.
License:
CrossDocker's own code is MIT licensed (see LICENSE).
It also uses third-party work: an RMSD routine reduced from the BSD-2-Clause
rmsd project, adapters derived from
AutoDockTools (Copyright Michel F. Sanner / TSRI, MGLTools Software License
Agreement), and a bundled copy of AutoDock Vina in the release archive under
its own separate licence (vina_license.rtf).
Each component, its licence and the modifications made are listed in NOTICE.md.