BioInterface

BioInterface is a Biopython based package that extracts Protein-DNA interfaces in a PDB structures.

• Free software: MIT license

• Documentation: https://biointerface.readthedocs.io.

Get Started

This is a little tutorial on how to use the BioInterface package.

The official release is found in the Python Package Index (PyPI)

$ pip install biointerface

You can extract a single Protein-DNA interface from a single protein chain.

from Bio.PDB.MMCIFParser import MMCIFParser
from biointerface import Interface, build_interfaces

# parse and build structure with Biopython
parser = MMCIFParser()
structure = parser.get_structure(
    structure_id="1A02", filename="1a02-assembly1.cif"
)

# extract interface from a specific protein chain
face = Interface(
    structure=structure,
    protein_chain_id="F",
    search_radius=5.0
)
face

<Interface chains=F:BA contacts=258 search_radius=5.0>

Check the official documentation for more information.

Feaures

• Extract one specific Protein-DNA interface in a PDB structure, given a protein chain id;

• Extract all Protein-DNA interfaces in a PDB structure;

• Get all interacting residues in a interface;

• Get all interacting atoms in a interface;

• Interface data as pandas DataFrame;

• Get all continous protein-bound double-strand nucleic acids;

• Get nucleic acid binding domain;

TODO

• Don’t use chain ids: it ignores the case where a chain has both protein and nucleic

Credits

This package was created with Cookiecutter and the audreyr/cookiecutter-pypackage project template.