nnguyen19 / chainsaw

Chainsaw

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

bioRxiv

Installation

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 STRIDE_EXE variable in src/constants.py to point to the pymol executable.

Usage

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).