A coarse-grained model for disordered proteins under crowded conditions

This repository contains code and data for:

Rauh A.S., Tesei, G. & Lindorff-Larsen, K. (2025) A coarse-grained model for disordered proteins under crowded conditions. bioRxiv

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

Running CALVADOS simulations with PEG

PEG simulations can be run either with the code provided here or using the CALVADOS package (Example)

File structure

• data: Pandas DataFrames with processed data from the simulations.
• single_chain_PEG: Scripts used in parameter scan for reproduction of single-chain properties of linear PEG chains with different molecular weight.
• protein_crowding: Scripts used in for tuning $\lambda_{PEG}$ in a comparison with PEG-induced compaction of IDPs.
• ps_crowding: Scripts used to run PEG-crowding slab simulations for phase separation systems.
• figures.ipynb: Jupyter Notebook with code to reproduce the figures in the manuscript.