Chainsaw is a deep learning method for predicting protein domain boundaries for a given protein structure.
If you find Chainsaw useful in your research, please cite:
Chainsaw: protein domain segmentation with fully convolutional neural networks
Jude Wells, Alex Hawkins-Hooker, Nicola Bordin, Brooks Paige and Christine Orengo
1) install stride: source code and instructions are packaged in this repository in the
stride directory. You will need to compile stride and put the executable in your
path. Update the STRIDE_EXE variable in src/constants.py to point to the stride
executable.
2) install the python dependencies: pip install -r requirements.txt
3) test it's working by running python get_predictions.py --structure_file example_files/AF-A0A1W2PQ64-F1-model_v4.pdb --output results/test.tsv
by default the output will be saved in the results directory.
Optional:
To visualise the domain assignments, ensure that you have pymol installed and update the
PYMOL_EXE variable in src/constants.py to point to the pymol executable.
python get_predictions.py --structure_file /path/to/file.pdb
or
python get_predictions.py --structure_directory /path/to/pdb_or_mmcif_directory
Note that the output predicted boundaries are based on residue consecutive indexing starting from 1 (not based on pdb auth numbers).