PIGEON-FEATHER (Peptide ID Generation for Exchange Of Nuclei-Free Energy Assignment Through Hydrogen Exchange Rates): a method for calculating free energies of opening (∆Gop) at single- or near-single-amino acid resolution for protein ensembles of all sizes from hydrogen exchange/mass spectrometry (HX/MS) data.
PIGEON-FEATHER can be used from Jupyter Notebook (recommended), or by writing Python scripts. The documentation can be found at http://glasgowlab.org/PIGEON-FEATHER.
The tutorials notebooks could be found at docs/source/tutorials.
# install mamba
wget "https://github.com/conda-forge/miniforge/releases/latest/download/Mambaforge-$(uname)-$(uname -m).sh"
bash Mambaforge-$(uname)-$(uname -m).sh
# create a conda environment and install the required packages
conda create --name pigeon_feather python=3.11
conda activate pigeon_feather
conda install jupyterlab mdanalysis numba
conda install pymol-open-source
pip install pyopenms hdxrate
# clone the PIGEON-FEATHER repo
git clone https://github.com/glasgowlab/PIGEON-FEATHER.git
# clone the bayesian hdx iso repo
git clone https://github.com/lucl13/bayesian_hdx.git
cd PIGEON-FEATHER
pip install .
cd ../bayesian_hdx
pip install .
docker build -f docker/Dockerfile -t pigeon_feather:0.9 .
docker run -it -v $(pwd):/work -p 8889:8889 --rm pigeon_feather:0.9 jupyter-lab --port 8889
click the link in the terminal to open the jupyter notebook cd to example/docker_example click and run
NOTE: bayesian_hdx at the above link is a fork of the original repo at https://github.com/salilab/bayesian_hdx with some modifications to the code to make it compatible with the PIGEON-FEATHER and support for the isotopic envelope fitting.
If you use PIGEON-FEATHER in scientific work, please cite:
C. Lu*, M. L. Wells*, A. Reckers, and A. Glasgow, “Site-resolved energetic information from HX/MS experiments.” bioRxiv, 2024. (*equal contributions) link to preprint