a bio-/chemoinformatics pipeline for drug repositioning applied to schistosomiasis
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.
| 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, Dec 15 data freeze | 20/09/2016 |
| chembl_drugtargets.txt | ChEMBL drug targets; downloaded from ChEMBL, Dec 15 data freeze, fix newline character at 770/771 and 820/821 and 1263/1264 and 1386, 2109, 3180 | 20/09/2016 |
| chembl_uniprot_mapping.txt | ChEMBL uniprot mapping, chembl ID to UniProt codes; downloaded from the ChEMBL 21 release page: fftp://ftp.ebi.ac.uk/pub/databases/chembl/ChEMBLdb/releases/chembl_21/chembl_uniprot_mapping_new.txt | 20/09/2016 |
| small_molecule_target_ids_all.csv | DrugBank Drug Target Identifier/Small Molecule Drugs; downloaded from DrugBank (note, this is the 'all', not just small molecule) release: 2016-07-01, version 5.0.1 | 20/09/2016 |
| uniprot_pdb.csv | Uniprot to pdb mapping file; downloaded from SIFTS (if necessary, a tsv version is also available), generated 2016/09/10 | 20/09/2016 |
| lig_pairs.lst | pdb to ligand mapping file; downloaded from PDBsum downloads (if necessary, the het_pairs.lst version is also available) | 20/09/2016 |
| Components-smiles-oa.smi | chemical components dictionary in smiles format (OpenEye); downloaded from RCSB Ligand Expo Downloads, in the SMILES/InChi data files (if necessary, stereo versions and CACTVS-generated versions available) | 20/09/2016 |
| pointless_het.csv | contains list of 'pointless' het ligands, including aminoacids, nucleotides, metals and crystallographic solvets/aids, copied across from drug_repo | n/a |
| all.sdf | DrugBank drugs in sdf format; downloaded from DrugBankrelease: 2016-07-01, version 5.0.1 | 20/09/2016 |
| speclist.txt | taxonomic codes and mnemonic codes for all species; downloaded from UniProt Release: 2016_08, 07-Sep-2016 | 20/09/2016 |
| pdb_pfam_mapping.txt | PDB IDs to Pfam domains and residue numbers; downloaded from EBI, release: 10/30/15 | 20/09/2016 |
- Python 2.6.9
- BioPhython 1.6.8 - Freely available on the BioPython website. Modify swissprot init.py to fix uniprot brackets problem like so:
def _read_rn(reference, rn_temp):
rn_split = rn_temp.split()
rn = rn_split[0]
assert rn[0] == '[' and rn[-1] == ']', "Missing brackets %s" % rn
reference.number = int(rn[1:-1]) - ArchIndex/ArchSchema - kindly provided by Dr Laskowski. For more information, please visit the ArchSchema website, or read the main reference for ArchSchema
- SMSD (Small Molecule Subgraph Detector). For more information, please visit the SMSD website, the GitHub repository, or read the main reference for SMSD
- MODELLER, for homology modelling (only for step 10). See MODELLER website
- arch_schema_cath.tsv (UniProt IDs to CATH domains and residue numbers), to be downloaded from ftp://ftp.cbi.edu.cn/pub/database/gene3d/ (downloaded on 20/09/2016)
- clone the repository
- check requirements
- modify the config.py file according to your needs
- run the script (>python drug_repo.py)
Copyright © 2016 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
THIS IS A WORK IN PROGRESS. This is version 2 of the original drug_repo.
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.
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