Usage¶

To use BioInterface in a Python project:

import biointerface

Extract One Protein-DNA Interface¶

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

from Bio.PDB.PDBList import PDBList
from Bio.PDB.MMCIFParser import MMCIFParser
from biointerface import Interface

# retrive file from PDB using Biopython
pdbl = PDBList()
pdbl.retrieve_pdb_file(pdb_code="1A02", pdir=".")
pdbl.retrieve_assembly_file(pdb_code="1A02", assembly_num=1, pdir=".")
# ... or else use your own

# 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>

Extract All Protein-DNA Interfaces¶

You can also extract all Protein-DNA interface from an entire structure.

from biointerface import build_interfaces

face_list = build_interfaces(structure=structure, search_radius=5.0)
face_list

[<Interface chains=J:BA contacts=189 search_radius=5.0>,
 <Interface chains=F:BA contacts=258 search_radius=5.0>,
 <Interface chains=N:BA contacts=529 search_radius=5.0>]

Get All Interacting Residues¶

You can access all interacting residues in a Protein-DNA interface, both aminoacids and nucleotides.

face.get_aminoacids()

[<Residue ARG het=  resseq=144 icode= >,
 <Residue ALA het=  resseq=151 icode= >,
 <Residue ARG het=  resseq=158 icode= >,
 <Residue ASN het=  resseq=147 icode= >,
 <Residue LYS het=  resseq=148 icode= >,
 <Residue LYS het=  resseq=153 icode= >,
 <Residue SER het=  resseq=154 icode= >,
 <Residue ARG het=  resseq=155 icode= >,
 <Residue ALA het=  resseq=150 icode= >,
 <Residue ARG het=  resseq=143 icode= >,
 <Residue ARG het=  resseq=146 icode= >,
 <Residue ARG het=  resseq=157 icode= >]

face.get_nucleotides()

[<Residue DT het=  resseq=4015 icode= >,
 <Residue DC het=  resseq=4016 icode= >,
 <Residue DT het=  resseq=4014 icode= >,
 <Residue DG het=  resseq=5007 icode= >,
 <Residue DA het=  resseq=4017 icode= >,
 <Residue DT het=  resseq=4018 icode= >,
 <Residue DT het=  resseq=5006 icode= >,
 <Residue DC het=  resseq=5003 icode= >,
 <Residue DA het=  resseq=5005 icode= >,
 <Residue DG het=  resseq=4012 icode= >,
 <Residue DT het=  resseq=4013 icode= >,
 <Residue DT het=  resseq=5004 icode= >]

Get All Interacting Atoms¶

You can access all interacting atoms in a Protein-DNA interface.

First of all you can get all interacting atoms as atom pairs.

contacts = face.get_atomic_contacts()
contacts[:5]

[(<Atom C5'>, <Atom NZ>),
 (<Atom C5'>, <Atom CE>),
 (<Atom O5'>, <Atom NZ>),
 (<Atom O5'>, <Atom CE>),
 (<Atom O5'>, <Atom CD>)]

You can also get all Protein or DNA interacting atoms, independently.

atoms = face.get_protein_atoms()
atoms[:5]

[<Atom CZ>, <Atom N>, <Atom NE>, <Atom CD>, <Atom CG>]

atoms = face.get_dna_atoms()
atoms[:5]

[<Atom P>, <Atom C5'>, <Atom C6>, <Atom C5>, <Atom C4'>]

Interface Data as DataFrame¶

You can get all Protein-DNA interface features as a pandas DataFrame.

df = face.as_dataframe()
df.columns

Index(['protein_chain_id', 'prot_res_hetfield', 'prot_res_number',
   'prot_res_icode', 'prot_res_name', 'prot_atom_name', 'prot_atom_altloc',
   'prot_atom_element', 'prot_atom_coord_x', 'prot_atom_coord_y',
   'prot_atom_coord_z', 'dna_chain_id', 'dna_res_hetfield',
   'dna_res_number', 'dna_res_icode', 'dna_res_name', 'dna_atom_name',
   'dna_atom_altloc', 'dna_atom_element', 'dna_atom_coord_x',
   'dna_atom_coord_y', 'dna_atom_coord_z', 'euclidean_distance'],
  dtype='object')

df

    protein_chain_id prot_res_hetfield  prot_res_number  ... euclidean_distance
                F                                148  ...           4.458498
                F                                148  ...           3.964944
                F                                148  ...           4.066739
                F                                148  ...           3.271817
                F                                148  ...           4.217340
...              ...               ...              ...  ...                ...
              F                                154  ...           4.644194
              F                                150  ...           4.594888
              F                                150  ...           4.784895
              F                                157  ...           4.904832
              F                                157  ...           4.299844

[258 rows x 23 columns]

Protein-Bound Nucleic Acids¶

BioInterface can extract all double-strand nucleic acids bound by the input protein, as a DoubleStrandNucleicAcid class from the package PDBNucleicAcids.

bound_dsna_list = face.get_bound_double_strands()
bound_dsna = dsna_list[0]
bound_dsna

<DoubleStrandNucleicAcid type='dsDNA' i-th strand='A' j-th strand='B'
 length=9>

The DoubleStrandNucleicAcid class has other useful methods.

bound_dsna.get_i_strand().get_seq()

Seq('GTTTCATAG')