PyMissense create the plot and modified pdb as shown in the AlphaMissense Paper
Project description
pymissense
PyMissense creates the 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:
-
It generates a plot similar to Figure 3D of the AlphaMissense paper
-
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. One example could be:
For example, to reproduce Figure 3D (the middle one) and the generate the PDB shown in Figure 3F do:
wget https://files.rcsb.org/download/7UPI.pdb
pymissense Q9UQ13 out --maxacid 200 --pdbpath 7upi.pdb
Note that the displayed only the first 200 amino acids in the plots and showed the pathogencity in the experimental PDB 7upi
.
Contributions
This script was developed in collaboration with Tobias Raisch
Project details
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