Motifs play a crucial role in protein functions. For example, short linear motifs (SLiMs) are known to mediate protein–protein interactions. In our research projects, we study protein structures and identifying motifs is integral in understanding protein functional properties. With the recent revolution in the structural biology field, AlphaFold Database now contains predicted structures of almost all sequences deposed in the proteome database Uniprot. We can use the AlphaFold predicted structures to investigate motifs of interest on the structural level.

Our project is to create a tool that allows scientists to find and visualize motifs in their proteins of interest to get more insights about their function.

The program's input will be a UniProt sequence ID and the amino acid sequence of the motif. Our program will retrieve the protein sequence and a PDB file with the structure from the AlphaFold database, find the indicated motif, and visualize it using PyMOL. The output will be a PyMOL session file (.pse) with all proteins and their colored motifs.

You need to clone this repository.

git clone https://github.com/Bodya-Huri/AlphaFoldMotif afmotif
cd afmotif

Now, create a conda environment with all the requirements installed.

conda create -n afmotif
conda activate afmotif
conda install conda-forge::biopython
conda install conda-forge::pymol-open-source

First, activate the working environment.

conda activate afmotif

Then, launch the program.

python3 motif_finder.py -i Q9NT68 -m VM

python3 motif_finder.py -f data.txt -m VM

Run a test from the folder with def.py file.

pytest

You might need to install pytest first.

conda install pytest

Simona Manasra: https://mlkndt.github.io/

Bohdana Hurieva: https://bodya-huri.github.io/