xlms-tools 1.0.0

xlms-tools is a set of command line tools to apply crosslinking mass spectrometry (XL-MS) data to protein structure models.

xlms-tools

Description

xlms-tools is a set of command line tools to apply crosslinking mass spectrometry (XL-MS) data to protein structure models.

Setting up xlms-tools

After downloading or cloning this repository, download dependencies by running the following from the project directory:

$ pip3 install -r requirements.txt

Using xlms-tools

Currently, xlms-tools can be run in two modes. The first is to score how well a protein structure model agrees with XL-MS data, specified as a list crosslinks and monolinks derived from a XL-MS experiment.

To score how well a protein structure agrees with XL-MS data

1. Format crosslinks and monolinks into a text file with the following format:

2. Score protein structure model/s:

$ python xlms-tools.py -m score -l [list of crosslinks and/or monolinks] [PDB file]

Citations

When using xlms-tools, please cite: Manalastas-Cantos, K. et al. (2023) Modeling flexible protein structure with AlphaFold2 and cross-linking mass spectrometry. BioRxiv. https://doi.org/10.1101/2023.09.11.557128