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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

Bioinformatics

Installation

Ensure that python 3.8, 3.9, 3.10, or 3.11 is installed, then install dependencies with the command bash setup.sh

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.

Chainsaw is tested on Linux and MacOS. It may work on Windows but this is not guaranteed.

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).

Installation Troubleshooting

If setup.sh fails follow the instructions below:

  1. install stride: source code and instructions are packaged in this repository in the stride directory. See stride/README_stride for instructions.

  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.