Disorder

A set of tools and pipelines for molecular dynamics simulations of protein systems. This is mainly aimed at simulating instrinsically disordered proteins, though it is general enough to be used for any protein class.

Installation

First install conda, if it is not installed already.

Clone the repo from github:

git clone https://github.com/hmartiniano/Disorder

Create conda environment

cd disorder
conda env create -f environment.yml

Usage

0. Activate the conda environment:

conda activate -n disorder 

1. Edit notebooks/explore_variants.ipynb and input a gene of interest and, optionally, known mutations.

2. Run the structure prediction pipeline:

./scripts/run_af2.sh <fasta_files> 

3. Run the system setup for a given pipeline (atomistic or coarse-grained):

snakemake -s workflows/setup/md/Snakefile.aa 

4. cd to the working directory and use snakemake to run individual simulations:

cd $workdir 
cd $mutation
snakemake -c <number of cores>

5. Run the analysis scripts in the scripts directory:

Copyright

Copyright (c) 2022, Hugo Martiniano, Nuno Galamba

Acknowledgements

This software was produced wth support from BioISI.