📈 PyPLIMSTEX 📉

Python implementation of PLIMSTEX

This is a Python-based implementation of the approach to quantifying protein-ligand interaction by mass spectrometry, titration and H/D exchange (PLIMSTEX) proposed by Zhu et al., 2004.

⚠️ For now, only 1:1 protein-ligand stoichiometry can be analysed with this code, which was developed to analyse interactions of GPCRs with G proteins, a known 1:1 stoichiometry. The theoretical basis of 1:N stoichiometry is outlined in the 2004 paper by Zhu et al..

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📦 Installation

Pre-requisites

Python 3.11 or higher

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Downloading Conda

If you don't already have one, you can download Anaconda (or miniconda) from the official Anaconda website for access to a Python environment.

You would need to install git (pip install git) in your base environment if you don't already have it.

Installing in a clean Conda environment

conda create -y -n pyplimstex python=3.11
conda activate pyplimstex
pip install git+https://github.com/fooMatt/PyPLIMSTEX.git

✨ Quick start

You can modify to the template config.toml file in assets/.

Note that the user still needs to 'pre-process' the HDX-MS data in DynamX and export this as a cluster CSV file as this code is unable to read the raw HDX-MS data.

Then run:

pyplimstex --config path/to/config.toml (optionally: --workers NUM_WORKERS)

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Made at the Institut de Génomique Fonctionnelle, Montpellier

Granier-Mouillac Team

Matthew Chee, 2026