drugdata/D3R

Drug Design Data Resource is a suite of software to enable filtering, docking, and scoring of new sequences from wwpdb.

Drug Design Data Resource CELPP Runner

Drug Design Data Resource is a suite of software to enable filtering of new entries from wwpdb and scoring of CELPP participant submissions. This package runs on D3R servers to host the CELPP challenge. Participants in CELPP who use the D3R-provided workflow template, CELPPade, will need to install this package as it uses some shared scripts.

For more information on this package or how to begin participating in CELPP, please visit our wiki page:

https://github.com/drugdata/d3r/wiki

Compatibility

• Works with Python 2.6, 2.7

Dependencies

• argparse
• lockfile
• psutil
• biopython
• xlsxwriter
• ftpretty
• NCBI Blast (needed by blastnfilter.py)
• rdkit (needed by blastnfilter.py and proteinligprep.py)
• schrodinger (needed by proteinligprep.py, glidedocking.py, chimera_proteinligprep.py & vinadocking.py)
• babel (needed by chimera_proteinligprep.py)
• Autodock Vina & MGL Tools (needed by vinadocking.py)
• OpenEye Python with License (needed by blastnfilter.py symmetry filter and by evaluate.py)

Installation

pip install d3r

Usage

Run

celpprunner.py --help

License

See LICENSE.txt

Bugs

Please report them here

Acknowledgements

• This work is funded in part by NIH grant 1U01GM111528 from the National Institute of General Medical Sciences
• This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.