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

• 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
• slab_trajectories.tar.bz2 simulation trajectories of multimer formation
• multimers_trajectories.tar.bz2 direct-coexistence simulation trajectories

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

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