pymissense 1.0.2

PyMissense create the plot and modified pdb as shown in the AlphaMissense Paper

pymissense

PyMissense creates the pathogencity plot and modified pdb as shown in the AlphaMissense paper for custom proteins.

What it does

AlphaMissense allows you to identify regions in your amino acid chain that are critical for protein function. This skript does two things:

1. It generates a plot similar to Figure 3D of the AlphaMissense paper

   

2. It creates a modified PDB file where the temperature factor is replaced by the pathogencity predicted by AlphaMissense that allows you to visualize the effect with Chimerax, like Figure 3E of the paper:

   

It does so by replacing the bfactor in the PDB.

How to install

pip install pymissense

How to use it

Generate usage is:

usage: pymissense [-h] [--pdbpath PDBPATH] [--maxacid MAXACID] uniprot_id output_path

AlphaMissense plot and pdb generator

positional arguments:
  uniprot_id         UNIPROT ID
  output_path        Output folder

options:
  -h, --help         show this help message and exit
  --pdbpath PDBPATH  If defined, it will write the pathogencity as bfactor in that PDB. If its not defined or not existing it will instead download the alphafold predicted PDB (default: None)
  --maxacid MAXACID  Maximum squence number to use. (default: None)

You can provide the optional argument --pdbpath if you want to use an experimental PDB, otherwise it will instead download the alphafold predicted PDB.

For example, to reproduce Figure 3D (the middle one) and the generate the PDB shown in Figure 3E do:

wget https://files.rcsb.org/download/7UPI.pdb
pymissense Q9UQ13 out --maxacid 200 --pdbpath 7upi.pdb 

Note that they displayed only the first 200 amino acids in the plots and showed the pathogencity with the experimental PDB 7upi.

Contributions

This script was developed in collaboration with Tobias Raisch