PEPtide VIrtual SCREENing using PIPER and sblu. You can now run Cluspro Workflow locally.
git clone https://github.com/elvismartis/PepViScreen.git
# installing a new virtualenv
python3 -m venv </path>/piper
# Activate the virtualenv
source </path>/piper/bin/activate
# Install packages inside the virtualenv to avoid conflicts.
python3 -m pip install -r requirements.txt
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sblu: Python library and associated scripts for munging data files from ClusPro/FTMap/etc.. For more details, visit sblu - PyPI.
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Piper: FFT-based docking software used in ClusPro. It is available as a 64-bit executable for use on Linux systems. Obtain PIPER from the web server Cluspro. You need to register and download the Piper binary. PIPER is open-source for academic users ONLY
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prepare_for_piper.py: This Python script prepares the PDB file compatible with PIPER. This script is a modification of the prepare.py script bundled with the piper_package—the original bundled Python script and its dependencies on pdb2pqr-1.9.0 work only with Python 2.7. prepare_for_piper.py is a workaround for using the latest pdb2pqr and Python3. (Report any bugs by opening an issue)
To perform protein-protein or protein-peptide docking with PIPER and extract docked conformation as a PDB file.
sh run_multidocking.sh
To prepare the receptor protein, execute the following command before running "run_multidocking.sh". This needs to be done once for each Receptor structure. The output will be "XYZ_pnon.pdb". Place this file in a directory; the PATH to this directory needs to be added in the main BASH script at "REC="
$PIPER_HOME/prepare_for_piper.py XYZ.pdb