Usage¶

To use BioInterface in a Python project:

import biointerface

Extract All Protein-Nucleic Acid Interfaces¶

You can extract all Protein-Nucleic acids interfaces from an entire structure.

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

# retrive file from PDB using Biopython
pdbl = PDBList()
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"
)

face_builder = InterfaceBuilder(search_radius=4.0)
face_list = face_builder.build_interfaces(entity=structure)
face_list

[<Interface chains=N:B contacts=143 search_radius=4.0>,
 <Interface chains=F:AB contacts=73 search_radius=4.0>,
 <Interface chains=J:AB contacts=59 search_radius=4.0>]

Extract One Protein-Nucleic Acid Interface¶

You can also extract a single Protein-Nucleic Acid interface from a single protein chain.

# filter by protein chain
faces_filt = [face for face in face_list if face.get_aminoacids()[0].parent.id == "F"]
faces_filt

[<Interface chains=F:AB contacts=73 search_radius=4.0>]

Get All Interacting Residues¶

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

face = faces_filt[0]
face.get_aminoacids()

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

face.get_nucleotides()

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

Get All Interacting Atoms¶

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

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

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

[(<Atom C5'>, <Atom CE>),
 (<Atom O5'>, <Atom CE>),
 (<Atom OP2>, <Atom NZ>),
 (<Atom OP2>, <Atom CE>),
 (<Atom OP2>, <Atom CD>)]

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

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

[<Atom CA>, <Atom CD>, <Atom NH2>, <Atom O>, <Atom NE>]

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

[<Atom O5'>, <Atom O5'>, <Atom C3'>, <Atom C2'>, <Atom OP2>]

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 prot_res_icode  ... euclidean_distance
               F                                148                 ...           3.964944
               F                                148                 ...           3.271817
               F                                148                 ...           3.719538
               F                                148                 ...           3.183074
               F                                148                 ...           3.976905
..              ...               ...              ...            ...  ...                ...
              F                                150                 ...           3.279753
              F                                150                 ...           3.368906
              F                                150                 ...           3.584772
              F                                154                 ...           3.474709
              F                                154                 ...           3.930451

[73 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 = bound_dsna_list[0]
bound_dsna

<DoubleStrandNucleicAcid type='dsDNA' strand ids='A:B' length=7>

The DoubleStrandNucleicAcid class has other useful methods.

bound_dsna.get_i_strand().get_seq()

Seq('TTTCATA')

Nucleic Acid Binding Domain¶

BioInterface can extract the nucleic acid binding domain of the input protein by extracting the minimum protein subsequence, which contains all nucleic acid binding aminoacids.

bd = face.get_binding_domain()
bd.get_sequence()

Seq('RERNKMAAAKSRNRR')