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Open Source Science

https://github.com/kull-centre/_2025_rauh_phosphorylation

https://github.com/kull-centre/_2025_rauh_phosphorylation

Science Score: 34.0%

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    CITATION.cff file
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    Found codemeta.json file
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    DOI references
    Found 2 DOI reference(s) in README
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    Organization kull-centre has institutional domain (www1.bio.ku.dk)
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    Low similarity (6.8%) to scientific vocabulary
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Repository

Basic Info
  • Host: GitHub
  • Owner: KULL-Centre
  • License: gpl-3.0
  • Language: Jupyter Notebook
  • Default Branch: main
  • Size: 2.39 MB
Statistics
  • Stars: 0
  • Watchers: 2
  • Forks: 0
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Created 12 months ago · Last pushed 10 months ago
Metadata Files
Readme License

README.md

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.

Owner

  • Name: Linderstrøm-Lang Centre for Protein Science, University of Copenhagen
  • Login: KULL-Centre
  • Kind: organization
  • Location: Copenhagen, Denmark

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