Transmembrane - short project

Assignment and detection of a protein's transmembrane regions

WARNING DO NOT RUN THE SCRIPT IT LOOPS INFINITELY

Set up the environnement

clone this repository

git clone https://github.com/iphigenieG/transmembrane.git

go into the created directory

cd ./transmembrane

Install conda

Install miniconda

And for more speed install mamba:

conda install mamba -n base -c conda-forge

Create the transmembrane conda environnement

conda env create -f transmembrane.yml

or (recommended)

mamba create -f transmembrane.yml

Load the transmembrane conda environment:

conda activate transmembrane

Quit the conda environment when done:

conda deactivate

Exemple use to get started

Download a pdb file

For this exemple let's download the protein from this entry in the OPM database. Either download the pdb from your navigator or directly from the terminal like so:

wget https://files.rcsb.org/download/1JDM.pdb

Use the main script to search for transmembrane regions

The basic usage goes like this (after activating the conda environement as shown previously)

python main.py 1jdm.pdb

We can manually set the width of the membrane in angstrom (defaults to 14)

python main.py 1jdm.pdb 22