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_2023_garcia-cabau_cpeb4's Introduction

DOI

Molecular simulations of the N-terminal domain of CPEB4

This repository contains Python code, Jupyter Notebooks, and simulation data for reproducing the simulation results of the manuscript Kinetic stabilization of translation-repression condensates by a neuron-specific microexon

Layout

  • analyses.ipynb Jupyter Notebook to analyze all the simulation data and generate plots
  • direct-coexistence/ Data and Python code related to multi-chain simulations of the CALVADOS model in slab geometry. Simulations are performed using openMM v7.5
  • multimers/ Data and Python code related to multi-chain simulations of multimer formation. Simulations are performed using openMM v7.5 and analysed using OVITO Basic v3.7

Usage

To open the Notebooks, install Miniconda and make sure all required packages are installed by issuing the following terminal commands

    conda env create -f environment.yml
    source activate cpeb4
    jupyter-notebook

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