Drug repositioning
Branch: master
Clone or download
Fetching latest commit…
Cannot retrieve the latest commit at this time.
Permalink
Type Name Latest commit message Commit time
Failed to load latest commit information.
.gitignore
7_chembl_clust_excel.txt
Components-smiles-oe.smi
LICENSE.md
README.md
all.sdf
chembl_drugs.txt
chembl_drugtargets.txt
chembl_uniprot_mapping.txt
config.py
drug_repo.py
lig_pairs.lst
pdb_pfam_mapping.txt
pointless_het.csv
small_molecule_target_ids_all.csv
speclist.txt
uniprot_pdb.csv

README.md

drug_repo

a bio-/chemoinformatics pipeline for drug repositioning applied to schistosomiasis

drug_repo_img

Table of contents

FAQ

Q. What is drug repositioning?
A. The usage of a known drug for a different therapeutic indication. If you are not familiar with this at all, try Wikipedia
Q. What is schistosomiasis?
A. A very nasty parasitic disease affecting over 200 million people. Learn more about schistosomiasis on the World Health Organization website
Q. How does the tool work?
A. By mapping! known drugs -> their targets -> their domain architecture -> parasite targets
Q. I am reading this README on my local machine, why is the formatting all weird?
A. This README is formatted in GitHub markdown, please open it on GitHub. I will include an instructions-only plain text readme soon

Contents of repository

File Description Accession date
drug_repo.py Python script that reads input files (chemb/drugbank), filters data, extracts relevant info for mapping with domain architecture info. It is being developed at the moment. n/a
config.py configuration file n/a
README.md this readme file n/a
LICENSE.md license n/a
chembl_drugs.txt ChEMBL drugs; downloaded from ChEMBL 30/04/2014
chembl_drugtargets.txt ChEMBL drug targets; downloaded from ChEMBL, manually edited to strip a newline character at lines 383/384. 30/04/2014
chembl_uniprot_mapping.txt ChEMBL uniprot mapping, chembl ID to UniProt codes; downloaded from the ChEMBL 18 release page: ftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_18/ 25/04/2014
small_molecule_target_ids_all.csv DrugBank Drug Target Identifier/Small Molecule Drugs; downloaded from DrugBank (if necessary, all_target_ids_all.csv is also available) 06/05/2014
uniprot_pdb.csv Uniprot to pdb mapping file; downloaded from SIFTS (if necessary, a tsv version is also available) 12/06/2014
lig_pairs.lst pdb to ligand mapping file; downloaded from PDBsum downloads (if necessary, the het_pairs.lst version is also available) 17/06/2014
Components-smiles-oa.smi chemical components dictionary in smiles format; downloaded from RCSB Ligand Expo Downloads, in the SMILES/InChi data files (if necessary, stereo versions and CACTVS-generated versions available) 20/06/2014
pointless_het.csv contains list of 'pointless' het ligands, including aminoacids, nucleotides, metals and crystallographic solvets/aids n/a
all.sdf DrugBank drugs in sdf format; downloaded from DrugBank 16/07/2014
speclist.txt taxonomic codes and mnemonic codes for all species; downloaded from UniProt 07/06/2014
pdb_pfam_mapping.txt PDB IDs to Pfam domains and residue numbers; downloaded from ftp://ftp.ebi.ac.uk/pub/databases/Pfam/mappings/ 20/08/2014

Requirements

Instructions

  • clone the repository
  • check requirements
  • modify the config.py file according to your needs
  • run the script (>python drug_repo.py)

License

Copyright © 2014 Sandra Giuliani
This repository is licensed under the terms of the MIT license. Please see the license file for more information. The MIT license is approved by the Open Source Initiative

Disclaimer

THIS IS A WORK IN PROGRESS. The main script (drug_repo.py) is currently being developed at the London School of Hygiene and Tropical Medicine, under the supervision of Dr Nick Furnham.

Contact

Feedback is very welcome, please drop me a line at: sandraxgiuliani [at] gmail [dot] com
You might also want to follow me on Twitter @sandygiuliani or visit my personal website.