PyMut: A rotamer based mutation library implemented in Python
PyMUT offers a fast and reliable way to introduce mutations using the Biopython
git clone https://github.com/gerdos/pyMUT
cd pyMUT
python3 mutate.py test/5e0m.pdb A 44 TYR
If you want to use PyMUT as a python library (recommended) close the repository and place its location inside your $PYTHON_PATH environment variable
from pymut import *
from Bio.PDB.PDBIO import PDBIO
from Bio.PDB import PDBParser
parser = PDBParser(QUIET=1)
structure = parser.get_structure("my_structure", "5e0m.pdb")
all_atoms = list(structure.get_atoms())
mutate(structure, 'A', 44, 'TYR', mutation_type='first')
io = PDBIO()
io.set_structure(structure)
io.save("test.pdb")
The resulting PDB file will contain the mutation. Please note, that resulting PDB file will only contain ATOM coordinates.
| Original residue | Mutated residue |
|---|---|
 |
 |
The mutate function takes the following arguments
| Parameter | Type | Default | Description | Required |
|---|---|---|---|---|
| chain | str | - | Chain identifier of the residue you want to mutate | Yes |
| resnum | int | - | Position of the residue you want to mutate in the PDB file | Yes |
| mutate_to | str | - | 3 letter IUPAC amino acid code (only the 20 standard residues are available) | Yes |
| rotamer_lib | object | None | Preloaded rotamer library returned from the load_rotamers function. If not given, it will be loaded separately for each PDB mutation call |
No |
| mutation_type | str | 'first' | How to select the rotamer. 3 possible options: first: Select the most likely rotamer based on probability in the library. random: Select a rotamer randomly based on the probability in the library. best: Select the best rotamer based on VdW energy. bestother: Select best rotamer based on VdW energy only considering atoms in other chains |
No |
PyMUT requires numpy and Biopython. The current implementation was tested on version 1.19.3+ and 1.7+ respectively
To install numpy on a standard Linux system
pip3 install numpy
pip3 install biopython
The algorithm assumes continuous neighboring residues, which is required for the dihedral calculations.
N and C terminal residues should be omitted, as the PHI and PSI angles are not defined. The algorithm will assume 0 for the missing degree
This project is licensed under the terms of the MIT license.
The rotamer library is based on the following article:
A Smoothed Backbone-Dependent Rotamer Library for Proteins Derived from Adaptive Kernel Density Estimates and Regressions Maxim V. Shapovalov Roland L. Dunbrack Jr.
The rotamer library is licensed by Creative Commons CC BY 4.0 license, and can be freely used, modified and distributed.