biointerface package

Submodules

biointerface.core module

Core module for extracting Protein-nucleic acid interfaces.

class biointerface.core.Interface(pp_atoms: list[Atom], na_atoms: list[Atom], search_radius: int | float = 4.0, pp_list: list[Polypeptide] = [], na_list: list[NucleicAcid] = [], dsna_list: list[DoubleStrandNucleicAcid] = [])[source]

Bases: object

Class for Protein-nucleic acid interface.

Parameters:

  • pp_atoms (list[Atom]) – Protein atoms.

  • na_atoms (list[Atom]) – Nucleic atoms.

  • search_radius (float | int) – Search radius, measured in Angstrom, within which Protein-nucleic acid interactions are found. Default is 4.0.

  • pp_list (list[Polypeptide]) – List of proteins found in the entity given to the builder. Default is an empty list.

  • na_list (list[NucleicAcid]) – List of nucleic acids found in the entity given to the builder. Default is an empty list.

  • dsna_list (list[DoubleStrandNucleicAcid]) – List of double stranded nucleic acids found in the entity given to the builder. Default is an empty list.

as_dataframe() → DataFrame[source]

Get all data from the interface, as a dataframe.

Contains the following data fields:

Residue hetero field Residue number Residue insertion code Residue name Atom name Atom alternate location Atom element Atomic coordinates (x, y, z) From both protein and nucleic acid atoms Euclidean distance between atom pair in contact

Returns

dfpd.DataFrame

All data from the interface.

get_aminoacids() → list[Residue][source]

Get only protein residues in the protein-nucleic acid interface.

Returns

list[Residue]

List of protein residues in the interface.

get_atomic_contacts() → list[tuple[Atom, Atom]][source]

Get interface contacts as pairs of atoms.

Returns

list[tuple[Atom, Atom]]

List of pairs of atoms, first one is from the nucleic acids, second one is from the protein.

get_binding_domains(upstream_pad: int = 0, downstream_pad: int = 0) → list[Polypeptide][source]

Get nucleic acid binding domains from the binding proteins.

The output is the binding “gapped” subsequence of the full protein found in the structure.

This method allows for “gaps” of unbound aminoacids inside the binding domain, only the aminoacids at the ends are trimmed according to being bound to nucleic acids (NAs) or not.

A visual example of “gaps”:

` Input full protein:          MQMLLNHKPTKFNGAIDERFHWKVIQRISGSEG NA-bound:                               ****  ** Output binding domain:                  FNGAIDER `

This method is only an inference of the NA-binding domain: while the output will likely align with the annotated true domain, it’ll likely not infer the whole domain. This is because a domain is defined by folding properties, while this method is much more naive. This is why I implemented some “padding” on both ends of the binding domain, it allows to be more lenient of the extent of the binding domain.

Parameters:

  • upstream_pad (int) – Number of non-binding residues, upstream of the first binding residue, to take inside the binding domain. Allows some leniency on what is considered a binding domain.

  • downstream_pad (int) – Number of non-binding residues, downstream of the last binding residue, to take inside the binding domain. Allows some leniency on what is considered a binding domain.

Returns

list[Polypeptide]

List of nucleic acid binding domains.

get_binding_proteins() → list[Polypeptide][source]

Get all nucleic acid binding proteins.

Returns

list[Polypeptide]

List of nucleic acid binding proteins.

get_bound_double_strands() → list[DoubleStrandNucleicAcid][source]

Get all double strand nucleic acids bound by the protein.

Returns

list[DoubleStrandNucleicAcid]

List of double strand nucleic acids bound by the protein.

get_bound_nucleic_acids() → list[NucleicAcid][source]

Get all nucleic acids bound by the protein.

Returns

list[NucleicAcid]

List of nucleic acids bound by the protein.

get_nucleic_acid_atoms() → list[Atom][source]

Get only nucleic acid atoms in the protein-nucleic acid interface.

Returns

list[Atom]

List of nucleic acid atoms in the interface.

get_nucleotides() → list[Residue][source]

Get only nucleic acid residues in the protein-nucleic acid interface.

Returns

list[Residue]

List of nucleic acid residues in the interface.

get_protein_atoms() → list[Atom][source]

Get only protein atoms in the protein-nucleic acid interface.

Returns

list[Atom]

List of protein atoms in the interface.

get_trimmed_double_strands() → list[DoubleStrandNucleicAcid][source]

Get all double-strand nucleic acids bound by the protein, but trimmed by binding.

The output double stranded nucleic acids (DSNAs) are subsequences of the full DSNAs found in the structure, since proteins usually do not bind the whole DSNA found in a PDB structure.

This method allows for “gaps” of unbound base pairs inside the DSNA, only the base pairs at the ends are trimmed according to being protein-bound or not.

A visual example of “gaps”:

``` Input full DSNA: GATATACAAGCCA

TGGCTTGTATATC

Protein-bound: **** ** Output protein-bound DSNA: TATACAAG

CTTGTATA

```

Returns

list[DoubleStrandNucleicAcid]

List of double stranded nucleic acids bound by the protein, but trimmed by binding.

get_trimmed_nucleic_acids() → list[NucleicAcid][source]

Get all nucleic acids bound by the protein, but trimmed by binding.

The output nucleic acids (NAs) are subsequences of the full NAs found in the structure, since proteins might not bind the whole NA.

This method allows for “gaps” of unbound nucleotides inside the NA, only the nucleotides at the ends are trimmed according to being protein-bound or not.

A visual example of “gaps”:

` Input full NA:            GATATACAAGCCA Protein-bound:              ****  ** Output protein-bound NA:    TATACAAG `

Returns

list[NucleicAcid]

List of nucleic acids bound by the protein, but trimmed by binding.

class biointerface.core.InterfaceBuilder(search_radius: float | int = 4.0, pp_builder: PPBuilder = <Bio.PDB.Polypeptide.PPBuilder object>, na_builder: NABuilder = <PDBNucleicAcids.NucleicAcid.NABuilder object>, dsna_builder: DSNABuilder = <PDBNucleicAcids.NucleicAcid.DSNABuilder object>)[source]

Bases: object

Use atomic distance to find Protein-Nucleic acid interfaces.

Assuming you only want standard nucleotides and amino acids.

Parameters

search_radiusfloat | int, optional

Search radius, measured in Angstrom, within which Protein-Nucleic acid interactions are found. Default is 4.0

pp_builderPPBuilder, optional

Polypeptide builder class from Biopython. Default is PPBuilder with default parameters.

na_builderNABuilder, optional

Polypeptide builder class from PDBNucleicAcids. Default is NABuilder with default parameters.

dsna_builderDSNABuilder, optional

Polypeptide builder class from PDBNucleicAcids. Default is DSNABuilder with default parameters.

build_interfaces(entity: Structure | Model | Chain, by: Literal['polypeptide', 'chain', 'structure']='polypeptide', standard_aminoacids: bool = True, standard_nucleotides: bool = True, pairing_rules: BasePairRules = <PDBNucleicAcids.BasePairRules.WatsonCrickBasePairRules object>) → list[Interface][source]

Extract all Protein-Nucleic acid interfaces found in a PDB entity.

Parameters

entityL{Structure}, L{Model} or L{Chain}

Protein-nucleic acid interfaces are searched for in this object. L{Structure} is the suggested input.

by: str, optional

If ‘polypeptide’, interfaces are extracted between nucleic acids bound by one polypeptide. If ‘chain’, interfaces are extracted between nucleic acids bound by one protein chain, composed by one or more polypeptides. If ‘structure’, interfaces are extracted between nucleic acids bound by all protein chains present in the structure, composed by one or more polypeptides. Most likely several polypeptides.

standard_aminoacids: bool, optional

Use only standard aminoacids. This is the aa_only parameter in the PPBuilder.build_peptides() method. Default is True.

standard_nucleotides: bool, optional

Use only standard nucleotides. This parameter is used in the NABuilder.build_nucleic_acids() method and in the DSNABuilder.build_double_strands() method. Default is True.

pairing_rulesoptional

Rules for proper base pairing class instance from PDBNucleicAcids. This parameter is used in the DSNABuilder.build_double_strands() method. Default is WatsonCrickBasePairRules() with default parameters.

Raises

PDBConstructionException: In case there is no protein

in the input entity.

PDBConstructionException: In case there is no nucleic acid

in the input entity.

Returns

list[Interface]

List of all Protein-Nucleic acid interfaces found in a PDB entity.

biointerface.core.concat_polypeptides(pp_list: list[Polypeptide]) → list[Polypeptide][source]

Module contents

Top-level package for BioInterface.

class biointerface.Interface(pp_atoms: list[Atom], na_atoms: list[Atom], search_radius: int | float = 4.0, pp_list: list[Polypeptide] = [], na_list: list[NucleicAcid] = [], dsna_list: list[DoubleStrandNucleicAcid] = [])[source]

Bases: object

Class for Protein-nucleic acid interface.

Parameters:

  • pp_atoms (list[Atom]) – Protein atoms.

  • na_atoms (list[Atom]) – Nucleic atoms.

  • search_radius (float | int) – Search radius, measured in Angstrom, within which Protein-nucleic acid interactions are found. Default is 4.0.

  • pp_list (list[Polypeptide]) – List of proteins found in the entity given to the builder. Default is an empty list.

  • na_list (list[NucleicAcid]) – List of nucleic acids found in the entity given to the builder. Default is an empty list.

  • dsna_list (list[DoubleStrandNucleicAcid]) – List of double stranded nucleic acids found in the entity given to the builder. Default is an empty list.

as_dataframe() → DataFrame[source]

Get all data from the interface, as a dataframe.

Contains the following data fields:

Residue hetero field Residue number Residue insertion code Residue name Atom name Atom alternate location Atom element Atomic coordinates (x, y, z) From both protein and nucleic acid atoms Euclidean distance between atom pair in contact

Returns

dfpd.DataFrame

All data from the interface.

get_aminoacids() → list[Residue][source]

Get only protein residues in the protein-nucleic acid interface.

Returns

list[Residue]

List of protein residues in the interface.

get_atomic_contacts() → list[tuple[Atom, Atom]][source]

Get interface contacts as pairs of atoms.

Returns

list[tuple[Atom, Atom]]

List of pairs of atoms, first one is from the nucleic acids, second one is from the protein.

get_binding_domains(upstream_pad: int = 0, downstream_pad: int = 0) → list[Polypeptide][source]

Get nucleic acid binding domains from the binding proteins.

The output is the binding “gapped” subsequence of the full protein found in the structure.

This method allows for “gaps” of unbound aminoacids inside the binding domain, only the aminoacids at the ends are trimmed according to being bound to nucleic acids (NAs) or not.

A visual example of “gaps”:

` Input full protein:          MQMLLNHKPTKFNGAIDERFHWKVIQRISGSEG NA-bound:                               ****  ** Output binding domain:                  FNGAIDER `

This method is only an inference of the NA-binding domain: while the output will likely align with the annotated true domain, it’ll likely not infer the whole domain. This is because a domain is defined by folding properties, while this method is much more naive. This is why I implemented some “padding” on both ends of the binding domain, it allows to be more lenient of the extent of the binding domain.

Parameters:

  • upstream_pad (int) – Number of non-binding residues, upstream of the first binding residue, to take inside the binding domain. Allows some leniency on what is considered a binding domain.

  • downstream_pad (int) – Number of non-binding residues, downstream of the last binding residue, to take inside the binding domain. Allows some leniency on what is considered a binding domain.

Returns

list[Polypeptide]

List of nucleic acid binding domains.

get_binding_proteins() → list[Polypeptide][source]

Get all nucleic acid binding proteins.

Returns

list[Polypeptide]

List of nucleic acid binding proteins.

get_bound_double_strands() → list[DoubleStrandNucleicAcid][source]

Get all double strand nucleic acids bound by the protein.

Returns

list[DoubleStrandNucleicAcid]

List of double strand nucleic acids bound by the protein.

get_bound_nucleic_acids() → list[NucleicAcid][source]

Get all nucleic acids bound by the protein.

Returns

list[NucleicAcid]

List of nucleic acids bound by the protein.

get_nucleic_acid_atoms() → list[Atom][source]

Get only nucleic acid atoms in the protein-nucleic acid interface.

Returns

list[Atom]

List of nucleic acid atoms in the interface.

get_nucleotides() → list[Residue][source]

Get only nucleic acid residues in the protein-nucleic acid interface.

Returns

list[Residue]

List of nucleic acid residues in the interface.

get_protein_atoms() → list[Atom][source]

Get only protein atoms in the protein-nucleic acid interface.

Returns

list[Atom]

List of protein atoms in the interface.

get_trimmed_double_strands() → list[DoubleStrandNucleicAcid][source]

Get all double-strand nucleic acids bound by the protein, but trimmed by binding.

The output double stranded nucleic acids (DSNAs) are subsequences of the full DSNAs found in the structure, since proteins usually do not bind the whole DSNA found in a PDB structure.

This method allows for “gaps” of unbound base pairs inside the DSNA, only the base pairs at the ends are trimmed according to being protein-bound or not.

A visual example of “gaps”:

``` Input full DSNA: GATATACAAGCCA

TGGCTTGTATATC

Protein-bound: **** ** Output protein-bound DSNA: TATACAAG

CTTGTATA

```

Returns

list[DoubleStrandNucleicAcid]

List of double stranded nucleic acids bound by the protein, but trimmed by binding.

get_trimmed_nucleic_acids() → list[NucleicAcid][source]

Get all nucleic acids bound by the protein, but trimmed by binding.

The output nucleic acids (NAs) are subsequences of the full NAs found in the structure, since proteins might not bind the whole NA.

This method allows for “gaps” of unbound nucleotides inside the NA, only the nucleotides at the ends are trimmed according to being protein-bound or not.

A visual example of “gaps”:

` Input full NA:            GATATACAAGCCA Protein-bound:              ****  ** Output protein-bound NA:    TATACAAG `

Returns

list[NucleicAcid]

List of nucleic acids bound by the protein, but trimmed by binding.

class biointerface.InterfaceBuilder(search_radius: float | int = 4.0, pp_builder: PPBuilder = <Bio.PDB.Polypeptide.PPBuilder object>, na_builder: NABuilder = <PDBNucleicAcids.NucleicAcid.NABuilder object>, dsna_builder: DSNABuilder = <PDBNucleicAcids.NucleicAcid.DSNABuilder object>)[source]

Bases: object

Use atomic distance to find Protein-Nucleic acid interfaces.

Assuming you only want standard nucleotides and amino acids.

Parameters

search_radiusfloat | int, optional

Search radius, measured in Angstrom, within which Protein-Nucleic acid interactions are found. Default is 4.0

pp_builderPPBuilder, optional

Polypeptide builder class from Biopython. Default is PPBuilder with default parameters.

na_builderNABuilder, optional

Polypeptide builder class from PDBNucleicAcids. Default is NABuilder with default parameters.

dsna_builderDSNABuilder, optional

Polypeptide builder class from PDBNucleicAcids. Default is DSNABuilder with default parameters.

build_interfaces(entity: Structure | Model | Chain, by: Literal['polypeptide', 'chain', 'structure']='polypeptide', standard_aminoacids: bool = True, standard_nucleotides: bool = True, pairing_rules: BasePairRules = <PDBNucleicAcids.BasePairRules.WatsonCrickBasePairRules object>) → list[Interface][source]

Extract all Protein-Nucleic acid interfaces found in a PDB entity.

Parameters

entityL{Structure}, L{Model} or L{Chain}

Protein-nucleic acid interfaces are searched for in this object. L{Structure} is the suggested input.

by: str, optional

If ‘polypeptide’, interfaces are extracted between nucleic acids bound by one polypeptide. If ‘chain’, interfaces are extracted between nucleic acids bound by one protein chain, composed by one or more polypeptides. If ‘structure’, interfaces are extracted between nucleic acids bound by all protein chains present in the structure, composed by one or more polypeptides. Most likely several polypeptides.

standard_aminoacids: bool, optional

Use only standard aminoacids. This is the aa_only parameter in the PPBuilder.build_peptides() method. Default is True.

standard_nucleotides: bool, optional

Use only standard nucleotides. This parameter is used in the NABuilder.build_nucleic_acids() method and in the DSNABuilder.build_double_strands() method. Default is True.

pairing_rulesoptional

Rules for proper base pairing class instance from PDBNucleicAcids. This parameter is used in the DSNABuilder.build_double_strands() method. Default is WatsonCrickBasePairRules() with default parameters.

Raises

PDBConstructionException: In case there is no protein

in the input entity.

PDBConstructionException: In case there is no nucleic acid

in the input entity.

Returns

list[Interface]

List of all Protein-Nucleic acid interfaces found in a PDB entity.

biointerface.concat_polypeptides(pp_list: list[Polypeptide]) → list[Polypeptide][source]