Package for the computation of distances from a residue to the catalytic active residues.
Project description
Mutation_Checker
Python package for checking the distance of a mutation from an active center of a protein.
Installation
Run the following to install:
pip install MutationChecker
Usage
Several function exists in this package, the main ones are
GeneToUniprotMapper
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 import GeneToUniprotMapper
GeneToPDBMapper("EIF2B5")
GeneToPDBMapper
This function takes the name of a gene and maps it into a PDB ID. By default uses the human specie.
@ input - gene (str) Name of Gene @ input - specie (str) Name of the Specie. Default: Human @ output - PDB ID (str) - PDB ID Code
Example: Generate PDB Code for EIF2B5 gene
from MutationChecker import GeneToPDBMapper
GeneToPDBMapper("EIF2B5")
PDBIDtoFile
This function takes a PDB Code and downloads the file into the working folder. It accepts a list of PDB to download the first available.
@ input - List of Strings - Code of PDBs @ output - PDB ID (str) - Path of the downloaded file.
Example: Download 1UBQ
from MutationChecker import PDBIDtoFile
PDBIDtoFile("1UBQ")
ExtractPDBSequence
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 import ExtractPDBSequence
ExtractPDBSequence(["./1UBQ"])
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 import GeneToFasta
GeneToFasta("EIF2B5")
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 import GeneToUniprotMapper, GeneToFasta
UniprotID = GeneToUniprotMapper("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 import CheckDistanceToActiveSite
CheckDistanceToActiveSite("LTA4H")
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