PeptoGrid is a set of tools implementing rescoring function for AutoDock Vina scoring predictions
PeptoGrid written in Python2.7 and depends on several other projects:
NumPy for calculations
H5PY for efficient data storage
ODDT for processing structural data
OpenBabel as a backend for ODDT
PyMOL for visualization
Python dependencies can be installed with pip:
pip install numpy h5py oddt
OpenBabel should be installed with your package manager or with any other suitable way
For Ubuntu/Debian users:
apt-get install libopenbabel4v5 python-openbabel
PyMOL can be download from official site or installed with package manager.
For Ubuntu/Debian users:
apt-get install pymol
PeptoGrid itself doesn't require any installation. Just clone or download repository and it's ready to go
No preprocessing (splitting or conversion to PDB) of AutoDock Vina results is required. PeptoGrid works with raw pdbqt outputs.
To build atom frequency grid:
python peptogrid/grid.py -m grid.hdf5 -f *out.pdbqt -c vina.cfg -s 0.1
To rescore poses:
python peptogrid/score.py -m grid.hdf5 -f *out.pdbqt -c vina.cfg -s 0.1 -o score_table.csv
To visualize in PyMOL:
- run PyMOL
- in command line type in following command:
run peptogrid/load_grid.py
- load calculated grid:
load_grid grid.hdf5
For details about volumetric data in PyMOL refer to PyMOL Wiki