A coarse-grained model for simulations of phosphorylated disordered proteins

This repository contains code and data for:

Rauh A.S., Hedemark G., Tesei, G. & Lindorff-Larsen, K. (2025) A coarse-grained model for simulations of phosphorylated disordered proteins bioRxiv

The simulation data can be retrieved from the Electronic Research Data Archive at UCPH (ERDA): here

Running CALVADOS phosphorylation simulations

Simulations with phosphorylated residues can be run either with the code provided here or using the CALVADOS package (Example)

File structure

• processed_data: Pandas DataFrames with processed data from the simulations.
• code: Python scripts used in this study to run the simulations and perform the analysis.
• residue_files: Files containing the residue data for the different phosphorylation models used in this study.
• figures.ipynb: Jupyter Notebook with code to reproduce the figures in the manuscript.