This repository contains a program to find a motif (eg active site constellation) of interest in a protein structure. In order to find the motif, pseudoatom positions for each residues side chain are created. These represent the mean position of the catalytically important atoms of a side chain. The input needs to be a pdb file of the protein.

Software Requirements:

• Python3.10

optional:

• Anaconda or Miniconda

In order to install the required packages run:

python3 -m venv /PATH/TO/YOUR/VENV
source venv/bin/activate
pip install -r requirements.txt

In order to see all parameters run:

python3 run_search.py -h

Example usage for a catalytic triad where the distance is 4.0A between SER-HIS, 3.2A between SER-ASP and 5.9A between HIS-ASP:

python3 run_search.py -f /PATH/TO/PDB/FILE -m SER-HIS-ASP -d 4.0-3.2-5.9