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https://github.com/kull-centre/_2024_yasuda_rna

https://github.com/kull-centre/_2024_yasuda_rna

Science Score: 21.0%

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Repository

Basic Info
  • Host: GitHub
  • Owner: KULL-Centre
  • License: gpl-3.0
  • Language: Jupyter Notebook
  • Default Branch: main
  • Size: 28.3 MB
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  • Stars: 1
  • Watchers: 1
  • Forks: 0
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Created over 1 year ago · Last pushed 11 months ago
Metadata Files
Readme License

README.md

A coarse-grained model of disordered RNA for simulations of biomolecular condensates

This repository contains codes, raw data and parameter files that used to reproduce the results in "A coarse-grained model of disordered RNA for simulations of biomolecular condensates by Yasuda, I., von Bülow, S., Tesei, G., Yamamoto E., Yasuoka K. & Lindorff-Larsen, K. (2024)".

Layout

  • calvados/ Codes and installation guide to run CALVADOS 2-RNA simulation as implemented in this work.
  • analysis/ Scrtipts to run analysis
  • all-atom/ All-atom structures of UCAAUC from [Bergonzo ,C., Grishaev, A., Bottaro, S., RNA, 28, 937–946 (2022)], and HCG_models from [Pietrek, L. M., Stelzl, L. S., Hummer, G., J. Chem. Theory Comput., 20, 2246–2260 (2024).]
  • single-chain/ Input files into calvados for single chain simulations of polyR30
  • flory_exponent/ Input files to run single chain simulations of polyR10-100
  • 400-chain/ Input files into calvados for 400-chain simulations of polyR30
  • FUSRGG3/ Input files into calvados for FUSRGG simulations of polyR40
  • FUSRGG3-1bead Input files into calvados (CALVADOS package version) for FUSRGG simulations of polyR40 using one-bead-per-nucleotide model.
  • MED1/ Input files into calvados for MED1 simulations of polyR40
  • viewer1.ipynb Jupyter Notebook to produce plots for the paper figures (Figure 2).
  • viewer2.ipynb Jupyter Notebook to produce plots for the paper figures (Figures 3 and 4).
  • data/ Files to generarte figures

Simulations can be run using prepare_full.py python prepare_full.py cd {name}/{temperature}/ python run.py

Continuing simulation can be run in the same directory of previous simulation, python run.py

CALVADOS package information

This two-bead-per-nucleotide model is implemented in CALVADOS package. https://github.com/KULL-Centre/CALVADOS

Owner

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

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