Molecular simulations of the N-terminal domain of CPEB4

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

Layout

• _2023_Garcia-Cabau_CPEB4-1.3.zip contains:
  • 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 v.7.5
  • 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 v.3.7

Python code and Jupyter notebook are also available on GitHub at https://github.com/KULL-Centre/_2023_Garcia-Cabau_CPEB4.

Simulation trajectories are available at https://sid.erda.dk/sharelink/F59Ctrg7U2.

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