Table I.
Public Databases Relevant for Predicting Drug-Target Interactions
| Resource | Description | Data content |
Website | Ref. |
|---|---|---|---|---|
| Curated drug-target interactions | ||||
| DrugBank | A comprehensive resource that combines detailed drug (i.e., chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e., sequence, structure, and pathway) information | 8206 drug entries including 1991 FDA-approved small-molecule drugs, 207 FDA-approved biotech drugs, 93 nutraceuticals and over 6000 experimental drugs; | http://www.drugbank.ca/ | (18) |
| ChEMBL | A manually curated chemical database of bioactive molecules with drug-like properties | 11,019 targets; 1,592,191 compounds; 13,967,816 activities | https://www.ebi.ac.uk/chembldb/ | (11) |
| KEGG | A comprehensive resource, including drugs, genes, reactions, pathways, and diseases, for understanding high-level functions and utilities of the biological system | 17,840 compounds; 10,431 drugs; 20,620,439 genes | http://www.kegg.jp/kegg/ | (19) |
| Comparative Toxicogenomics Database (CTD) | A public website and research tool that curates scientific data describing relationships between chemicals/drugs, genes/proteins, diseases, taxa, phenotypes, GO annotations, pathways, and interaction modules | 1,379,105 chemical-gene interactions; 19,753,624 gene-disease associations; 2,060,371; 14,672 chemicals; 6401 diseases; 42,761 genes | http://ctdbase.org/ | (27) |
| Guide to PHARMACOLOGY | An open-access website, acting as a portal to information on the biological targets of licensed drugs and other small molecules | 2789 targets; 8611 ligands; 14,577 curated binding constants; 31,207 binding constants from large-scale screening | http://www.guidetopharmacology.org/ | (28) |
| Therapeutic Target Database (TTD) | A database to provide information about the known and explored therapeutic protein and nucleic acid targets, the targeted disease, pathway information, and the corresponding drugs directed at each of these targets | 2025 target; 17,816 drugs | http://bidd.nus.edu.sg/group/cjttd/ | (23) |
| STITCH | A resource to explore known and predicted interactions of chemicals and proteins | 300,000 small molecules; 2.6 million proteins; 1133 organisms | http://stitch.embl.de/ | (22) |
| SuperTarget | An extensive web resource for analyzing drug-target interactions | 6219 targets; 195,770 compounds; 332,828 drug-target interactions; 282 drug-target related pathways; 6532 drug-target related ontologies; 63 cytochromes | http://insilico.charite.de/supertarget/ | (21) |
| DrugKiNET | An open-access, online resource to foster the identification and characterization of inhibitors of protein kinases for academic and industrial research | 400 human kinases; 800 inhibitors; 105,000 kinase-compound pairs | http://www.drugkinet.ca/ | |
| PROMISCUOUS | An exhaustive resource of protein-protein and drug-protein interactions with the aim of providing a uniform dataset for drug repositioning and further analysis | 5258 drugs with targets; 6548 targets with drugs; 23,702 drug-target interactions | http://bioinformatics.charite.de/promiscuous/ | (29) |
| NCGC Pharmaceutical Collection | A comprehensive resource of clinically approved drugs enabling repurposing and chemical genomics | 14,814 compounds; 1270 targets | https://tripod.nih.gov/npc/ | (30) |
| ChemProt | A resource of annotated and predicted chemical-protein interactions | 1.7 million chemicals; 20,000 proteins | http://potentia.cbs.dtu.dk/ChemProt/ | (37) |
| BRENDA | The main enzyme and enzyme-ligand information system | 83,000 enzymes; 206,000 enzyme ligands | http://www.brenda-enzymes.org/ | (20) |
| MATADOR | A manually annotated targets and drug online resource | 1500 drugs; 2500 target proteins; 7300 drug-protein elations | http://matador.embl.de/ | (39) |
| 3D structures and/or binding affinities | ||||
| Protein Data Bank (PDB) | A crystallographic database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids | 120,642 biological macromolecular structures | http://www.rcsb.org/pdb/home/home.do | (31) |
| MMDB | A collection of publicly accessible experimentally determined macromolecular structures with added information on the biological function and the evolutionary history of macromolecules | 119,566 macromolecular structures, with 86,960 contains chemicals | https://www.ncbi.nlm.nih.gov/structure | (32) |
| PDBbind | A comprehensive collection of the experimentally measured binding affinity data for all types of biomolecular complexes deposited in the Protein Data Bank (PDB) | 14,620 biomolecular complexes, including protein-ligand (11,987), nucleic acid-ligand (109), protein-nucleic acid (717), and protein-protein complexes (1807) | http://www.pdbbind-cn.org/ | (33) |
| BindingDB | A public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of proteins considered to be candidate drug targets with ligands that are small, drug-like molecules | 1,242,569 binding data; 6395 protein targets, 547,013 small molecules | http://bindingdb.org/ | (25) |
| Binding MOAD | A collection of well-resolved protein crystal structures with clearly identified biologically relevant ligands annotated with experimentally determined binding data extracted from literature | 25,771 protein-ligand structures; 9142 binding data; 12,440 different ligands; 7599 different families | http://bindingmoad.org/ | (34) |
| PDSP Ki database | A unique resource in the public domain which provides information on the abilities of drugs to interact with an expanding number of molecular targets | 59,705 Ki values | http://kidbdev.med.unc.edu/databases/pdsp.php | (40) |
| Side effects | ||||
| SIDER | An information portal on marketed medicines and their recorded adverse drug reactions | 1430 drugs; 5868 side effects; 139,756 drug-side effect pairs | http://sideeffects.embl.de/ | (24) |
| FAERS | FDA’s adverse event reporting system | http://www.fda.gov/Drugs/GuidanceComplianceRegulatoryInformation/Surveillance/AdverseDrugEffects/default.htm | ||
| MetaADEDB | A comprehensive computer-available adverse drug events database | 3060 chemicals; 13,256 side effects; 527,216 drug-ADEs associations | http://lmmd.ecust.edu.cn/online_services/metaadedb/ | (38) |
| JAPIC | Side effects | http://www.japic.or.jp/ | ||
| Large screening programs and data repositories | ||||
| PubChem BioAssay | A public repository for bioactivity data of small molecules and RNAi reagents against thousands of molecular targets | 1.2 million bioassays; 3 million tested substances (2 million compounds); 250 million bioactivities; 10,000 protein targets | https://ncbi.nlm.nih.gov/pcassay/ | (8) (9) (10) |
| NCI/DTP | The Developmental Therapeutics Program of the National Cancer Institute | https://dtp.cancer.gov/ | (26) | |
| ChemBank | A public, web-based informatics environment for data derived from small molecules and small-molecule screens | http://chembank.broadinstitute.org/ | (35) | |
| Connectivity Map (CMap) | A catalog of gene expression data collected from human cells treated with chemical compounds and genetic reagents | 6100 gene expression profiles; 13,469 human genes; 1309 bioactive small compounds | https://www.broadinstitute.org/connectivity-map-cmap | (36) |