MutationChecker 0.1.7

Package for the computation of distances from a residue to the catalytic active residues.

Mutation_Checker

Python package for checking the distance of a mutation from an active center of a protein.

Installation

Run the following to install:

pip3 install MutationChecker

Usage

This package consists of several modules: MAPPER, EMBL, PROSITE and STRUCTURE. Each one has it's own methods.

MAPPER MODULE

The mapper module consist of 3 functions. GeneToUniprot, GeneToPDB and GeneToFasta. These functions are used for converting identifiers between main databases.

GeneToUniprot

This function takes the name of a gene and maps it into a Uniprot Reviewed ID. By default uses the human specie.

@ input - gene (str) Name of Gene @ input - specie (str) Name of the Specie. Default: Human @ output - Uniprot ID (str) - Uniprot ID Code

Example: Generate info for EIF2B5 gene

from MutationChecker.mapper import GeneToUniprot
GeneToUniprot("EIF2B5")

GeneToPDB

This function takes the name of a gene and maps it into a list of PDB id's By default uses the human specie.

@ input - gene (str) Name of Gene @ input - specie (str) Name of the Specie. Default: Human @ output - PDB ID (list of str) - PDB ID Codes

Example: Generate PDB Code for EIF2B5 gene

from MutationChecker.mapper import GeneToPDBMapper
GeneToPDB("EIF2B5")

GeneToFasta

This function takes the name of a gene, and extract its sequence from Uniprot.

@ input - gene (str) Name of Gene @ input - specie (str) Name of the Specie. Default: Human @ output - Uniprot Fasta (str)

Example: Generate Fasta for EIF2B5 gene

from MutationChecker.mapper import GeneToFasta
GeneToFasta("EIF2B5")

STRUCTURE MODULE

This module contains methods related to computations of the PDB structure file of a protein.

DownloadPDB

This function takes a list of str (or one str) of PDB Codes and downloads the file into the working folder. It accepts a list of PDB to download the longest PDB structure..

@ input - List of Strings (or standalone str) - Code of PDBs @ output - PDB ID (str) - Path of the downloaded file.

Example: Download 1UBQ

from MutationChecker.structure import DownloadPDB
DownloadPDB("1UBQ")

PDBtoSequence

This function takes a PDB file and extracts the sequence of the structure.

@ input - PDB File path (str) @ output - Fasta Sequence (str) - Sequence of the structure.

Example: Get sequence for 1UBQ file

from MutationChecker.structure import PDBtoSequence
ExtractPDBSequence("./1UBQ")

MapUniprotToPDB

This function takes a sequence of uniprot, a sequence of PDB (of the same protein) and a uniprot residue number, and returns you the residue number on the structure.

@ input - Uniprot Fasta (str), can be obtained with the method GeneToFasta @ input - PDB Fasta (str), can be obtained with the method PDBtoSequence @ input - uniprot residue number (int) @ output - PDB residue number that match the uniprot residue number given (int)

from MutationChecker.structure import MapUniprotToPDB
MapUniprotToPDB(GeneToFasta("EIF2B5"), PDBtoSequence("3JUI"), 45)

CheckDistances

This function takes a residue number , a list of another residue numbers, and a PDB structure file, and compute the physical distance between the first residue to the residues on the list

@ input - PDB residue number (int) @ input - List of PDB residue numbers (list) @ output - List of distances between the first input residue, to the ones in the list (float)

from MutationChecker.structure import CheckDistances
CheckDistances(1, [5, 6, 7], "./pdb3jui.ent")

PROSITE MODULE

This module has methods to search and parse the prosite database.

PrositeRequest

This function takes an uniprot id, and returns a JSON with information about the domains and motifs of the protein.

@ input - Uniprot ID (str) @ output - Information about protein domains (json)

from MutationChecker.prosite import PrositeRequest
PrositeRequest("Q13144")

CheckMutationProsite

This function takes a number of the residue in the sequence according to uniprot, and a uniprot ID of the protein. It search the Prosite database to extract the motifs, and checks if the mutation falls in place.

@ input - num_residue (int) - Number of the residue to check in the sequence uniprot_id (str) - String of the uniprot identifier of the protein to check.

@ output - Bool - The "num_residue" falls into the domain found by Prosite

from MutationChecker.prosite import CheckMutationProsite
CheckMutationProsite(45, "Q13144")

RetrieveDomain

This function takes a number of the residue in the sequence according to uniprot, and a uniprot ID of the protein. It search the Prosite database to extract the motifs, and checks if the mutation falls in place.

@ input - num_residue (int) - Number of the residue to check in the sequence uniprot_id (str) - String of the uniprot identifier of the protein to check.

@ output - tupple of str - Tupple with the parameters (Name of the domain found at num_residue, Accession code of Prosite of the domain.)

from MutationChecker.prosite import RetrieveDomain
RetrieveDomain(45, "Q13144")

EMBL MODULE

This module has function related to the parse of the active site described on EMBL

ObtainActiveCenterResidues

This function takes the Uniprot ID of a protein, and returns a list of residue numbers that conforms the active site based on EMBL-EBI

@ input - gene (str) Name of Gene @ output - List of Strings - Active Site residue numbers.

If the protein has not an active site mapped on EMBL-EBI it returns None.

Example: Get Active Site residues for LTA4H

from MutationChecker.embl import ObtainActiveCenterResidues
from MutationChecker.mapper import GeneToUniprot, GeneToFasta

UniprotID = GeneToUniprot("LTA4H")
ObtainActiveCenterResidues(UniprotID)

CheckDistanceToActiveSite

This function takes a name of the Gene, and a residue number, and computes the physical distance in amstrongs between the residue number and the active site residues.

@ input - gene (str) Name of the gene @ input - residue number (int) - Number of residue to check @ output - List of tupples (Name of active site residue, number)

Example: Get distances to the Active site from ASN488 in LTA4H

from MutationChecker.embl import CheckDistanceToActiveSite
CheckDistanceToActiveSite("LTA4H")