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Open Source Science

https://github.com/kull-centre/_2025_rauh_peg

https://github.com/kull-centre/_2025_rauh_peg

Science Score: 47.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
    Found .zenodo.json file
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    DOI references
    Found 2 DOI reference(s) in README
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    Academic publication links
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    Institutional organization owner
    Organization kull-centre has institutional domain (www1.bio.ku.dk)
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    JOSS paper metadata
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    Scientific vocabulary similarity
    Low similarity (6.8%) to scientific vocabulary
Last synced: 4 months ago · JSON representation

Repository

Basic Info
  • Host: GitHub
  • Owner: KULL-Centre
  • License: gpl-3.0
  • Language: Jupyter Notebook
  • Default Branch: main
  • Size: 64.8 MB
Statistics
  • Stars: 0
  • Watchers: 2
  • Forks: 0
  • Open Issues: 0
  • Releases: 0
Created about 1 year ago · Last pushed 9 months ago
Metadata Files
Readme License

README.md

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.
  • singlechainPEG: 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.

Owner

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

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