Analysis of PTMs in their structural context using the StructureMap and AlphaMap Python packages
This repository contains all data and python notebooks to reproduce the analyses presented in: "The structural context of PTMs at a proteome wide scale" by Bludau et al. (2022).
To set up the analysis, the first step is to run the commands in setup_environment.sh.
The actual analysis is performed in multiple jupyter notebooks:
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PTM data processing and import: notebooks in ptm_data_import
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Benchmark for IDR prediction: IDR_benchmark.ipynb
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Main structuremap analysis: data_analysis_structuremap.ipynb
This notebook is also available as HTML page, which displays all figures.
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Proteasome inhibitor usage in ubiquitination datasets on PhosphoSitePlus: PSP_Ubi.ipynb