mutatex_pipelines

Overview

This repository contains three Snakemake-based pipelines for peptide mutation scanning runs and processing with MutateX¹.

The first pipeline custom_scan includes two protocols:

• The protocol custom_scan/stability_scan predicts changes of folding free energy upon mutation for each residue of a given list of mutations provided as input. Each residue is mutated to a list of residue types depending on the mutations found in the corresponding input dataset.

• The protocol custom_scan/stability_binding_scan predicts changes of folding and binding free energy upon mutation for each residue of a given list of mutations provided as input. Each residue is mutated to a list of residue types depending on the mutations found in the corresponding input dataset.

The second pipeline custom_collect_scan behaves as custom_scan/stability_scan, but the user is not required to provide the input PDBs, instead the pipeline will automatically retrieve the structures from AlphaFold Protein Structure Database, if present, trim them based on user input and run the analysis.

The third pipeline custom_analysis visualizes the output of MutateX stability scans by running MutateX's plotting tools. These include the generation of: heatmaps, boxplots, scatter plots, average plots, violin plots, logo plots, density plots and output tables (.xlsx and .csv formats).

References

Footnotes

1. Tiberti, Terkelsen, T., Cremers, T. C., Di Marco, M., da Piedade, I., Maiani, E., & Papaleo, E. (2019). MutateX: an automated pipeline for in-silico saturation mutagenesis of protein structures and structural ensembles. https://doi.org/10.1101/824938 ↩