Chemical databases/resources
Chemical databases/resources are the backbone of computer-aided drug discovery, whether it is chemoinformatics or bioinformatics. These databases gives information which can be used to build knowledge-based models for discovering and designing drug molecules. Here, we have provides list of major databases that are freely available and widely used.
Chemical databases/web resources
| Database | Description |
|---|---|
| PubChem | PubChem is a database of chemical molecules which maintains three types of information namely, substance, compound and BioAssays. |
| ZINC | ZINC database contains 21 million compounds available for virtual screening. In this database various molecule features like molecular weight, logP etc are included. |
| ChEMBL | This database provides comprehensive information about 1 million bioactive (small drug-like molecules) compounds with 8200 drug targets. |
| NCI | NCI database had more than 275,000 small molecules structures, a very useful resource for researchers working in the filled of cancer/AIDS. |
| ChemDB | It is a databse of five million chemicals which contains information of chemicals that includes predicted or experimentally determined physicochemical properties, such as 3D structure, melting temperature and solubility. |
| ChemSpider | ChemSpider contains more than 28 million unique chemical entities aggregated from more than 400 diverse data sources. |
| BindingDB | It is a binding affinity database of small molecules which contains 910,836 binding data, for 6,263 protein targets and 378,980 small molecules. |
| PDB-Bind | It is a collection of binding affinities for protein-ligand complexes with known three-dimensional structures. It contains 5671 protein-ligand complexes. |
| PDBeChem | It provides comprehensive information of ligands, small molecules and monomers. Presently it consists 15502 ligands. |
| KEGG | It is a database resource that integrates genomic, chemical and systemic functional information. |
| HMDB | A database containing detailed information about small molecule metabolites found in the human body. |
| SMPDB | It is Small molecule Pathway database that containing more than 350 small-molecule pathways found in humans. |
| BIAdb | It is a comprehensive database of benzylisoquinoline alkaloids which contains information about 846 unique benzylisoquinoline alkaloids. |
| DrugBank | The database that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. The database contains 6712 drug entries including 1448 FDA-approved small molecule drugs, 131 FDA-approved biotech (protein/peptide) drugs, 85 nutraceuticals and 5080 experimental drugs. |
| HIT | HIT is a comprehensive database for protein targets for FDA-approved drugs as well as the promising precursors. It currently contains about 1,301 known protein targets(221 proteins are described as direct targets). |
| SuperNatural | A freely available database of approximately 50,000 natural compounds. |
| NPACT | It contains experimentally validated plant-derived natural compounds exhibiting anti-cancerous activity. Currently it contains 1574 compound entries. |
| TTD | This database 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. |
| PharmaGKB | It is a pharmacogenomics knowledge resource that encompasses clinical information of drug molecules. |
| SuperDrug | This database contains approximately 2500 3D-structures of active ingredients of essential marketed drugs. |