Table 2.
Databases for the identification of drug candidates for repositioning.
| Database | Description | Website | Citation |
|---|---|---|---|
| DGIdb | DGIdb contains 28,000 drug-gene interactions from 27 sources and can be queried by gene or drug. | http://dgidb.genome.wustl.edu/ | Wagner et al., 2016 |
| RE:fine Drugs | RE:fine provides a triad approach linking drugs to genes and disease at the same time as linking genes/variants to disease. The database contains 1,770 diseases, 916 drugs, and 567 genes and findings can be queried by drug, disease, or gene. | http://drug-repurposing.nationwidechildrens.org/ | Moosavinasab et al., 2016 |
| CMap | CMap is a library of nearly 500,000 gene expression signatures from human cell lines exposed chemical and genetic perturbation, and supports queries by gene and drug. The database also contains detailed drug information including known targets, stage of development and mechanism of action. | https://clue.io/ | Lamb et al., 2006 |
| DrugBank | DrugBank contains information on 9,591 FDA approved and experimental drugs with links to 4,661 targets. DrugBank supports general queries by drug, target, pathway and indication. | https://www.drugbank.ca/ | Law et al., 2014 |
| ChEMBL | ChEMBL contains 11,538 target and 2.1 million compound records that can be searched by ligand or target and browsed for drugs, targets or indications. | https://www.ebi.ac.uk/chembl/ | Gaulton et al., 2017 |
| PharmGKB | PharmGKB contains information on 621 drugs, 118 pathways and 474 pharmacogenetic labels as well as encompassing clinical information including gene-drug associations and genotype–phenotype relationships. PharmGKB can be queried for molecule, gene, variant, or combination. | https://www.pharmgkb.org/ | Whirl-Carrillo et al., 2012 |
| CTD | The Comparative Toxicogenomics Database (CTD) contains 34 million relationships between drugs (and other chemical entities) and genes/proteins. and can be queried by chemical, chemical-gene interaction, gene, gene form, disease, pathway, organism, or gene ontology. | http://ctdbase.org/ | Davis et al., 2017 |
| STITCH | STITCH is a database of known and predicted interactions between chemical entities and proteins, containing data from ∼500,000 chemicals, 9.6 million proteins and 1.6 billion interactions. The database supports queries by chemical, protein or gene name as well as by chemical structures or protein sequences. | http://stitch.embl.de/ | Szklarczyk et al., 2017 |
| BindingDB | BindingDB is a database of measured binding affinities focusing on the interactions of proteins considered to be drug-targets and small, drug-like molecules. It contains data for 7,225 protein targets and 621,060 small molecules. Searches can be conducted by small molecule, target, or assay. | http://bindingdb.org/bind/index.jsp | Gilson et al., 2016 |