Table 1.

Table of open-access resources available to the public for bioinformatics and chemoinformatics in drug discovery and toxicology.

Category	Database	Description
Drug	BindingDB ChEBI ChemBank ChEMBL DrugBank PharmGkb SuperTarget Therapeutic Target Database ZINC	Binding affinities of small, drug-like molecules to protein targets Small chemical compounds containing structural, nomenclature and ontology information Biomedical measurements derived from cell lines treated with small molecules Manually curated bioactive molecules with drug-like properties maintained by the EBI FDA-approved and experimental drugs with drug target, bio- and chemoinformatic data Pharmacogenomic-focused genetic, molecular, cellular and clinical data for drugs ~7300 drug–target associations with ~5000 manually annotated Known therapeutic protein targets with pathway information and corresponding drugs ~21 million compounds that are commercially available and prepared for virtual screening
Disease	National Organization of Rare Diseases Online Mendelian Inheritance of Man	NORD contains information on rare human diseases Catalog of human genes and genetic disorders maintained by the Johns Hopkins University
Protein–protein/–gene/–other interactions	BioGRID DGIdb ExPASy STRING MatrixDB MINT Database of Interacting Proteins	~730,000 raw protein and genetic interactions from major model organisms Drug gene interaction database curated from multiple well-established databases Known and predicted protein–protein interactions from experimental repositories and computational methods Interactions between extracellular proteins (i.e., collagen and laminins) and polysaccharides Molecular interaction database focusing on experimentally validated protein–protein interactions Manual and computational curation of experimentally determined protein–protein interactions
Genomics	Gene Expression Omnibus Oncomine The Cancer Genome Atlas UCSC Cancer Genome Browser G-DOC	Public functional array- and sequence-based genomics data repository Cancer microarray database that can be subdivided by treatment, patient survival and other demographics Large-scale genome sequencing platform for multiple cancers led by the NCI and the NHGRI Interactive annotated cancer genome-browser website hosted by the University of California, Santa Cruz Broad collection of bioinformatics and systems biology tools for analysis and visualization of four major ‘omics’ types: DNA, mRNA, microRNA and metabolites
Proteomics	dbDEPC GeMDBJ Proteomics Plasma Protein Database PRIDE The Human Protein Atlas UniProt	Database of differentially expressed proteins in human cancer Clinical and cell line protein LC-MS/MS and 2D-difference gel electrophoresis for expression levels Initiative of the Human Proteome Organization to characterize human plasma and serum proteome Centralized standards-compliant mass spectrometry proteomics and post-translational modifications Immunohistochemistry-based protein expression profiles of various human tissues, cancers and cell lines Comprehensive protein sequence and annotation data
Metabolomics	BiGG HMDB HumanCyc SMPDB	Genomic-based reconstruction of human metabolism for systems biology simulation and flux modeling Human small molecule metabolites with associated chemical, clinical and molecular biology information Human metabolic pathway/genome bioinformatics database constituting over 28,000 genes Small molecule pathway database with >400 unique human pathways not found in other databases
Toxicology	Chemical Effects in Biological Systems Comparative Toxicogenomics Database EPA ACToR FDA Adverse Event Reporting System OpenTox SIDER T3DB TOXNET	Developed by the National Institute of Environmental Health Sciences to house toxicology studies Curation of chemical–gene, chemical–disease, and gene–disease associations and constructs networks Aggregated Computational Toxicology Resource to query multiple EPA chemical toxicity databases Adverse event and medication error reports submitted to the FDA for post-market safety surveillance Interoperable framework for predictive toxicology and community platform for creation of applications Adverse drug reactions on marketed medicines extracted from public documents and package inserts ~37,000 pollutant–, pesticide– and food toxin–target associations with 50 related bioinformatics data fields Integrated database system of hazardous chemicals, toxic releases and environmental health by the NLM
Structural biology/ontology/enzymology/pathways	BRENDA Gene Ontology Ingenuity KEGG RCSB PDB Reactome SCOP	Comprehensive repository for molecular and biochemical information of enzymes classified by the IUBMB Gene and gene product annotations across multiple species with supported tools for analytics Web-based applications for analyzing genomic and pathway data Five databases that connect molecular interaction networks to recapitulate the human biological system The Protein Data Bank containing protein crystal structures and ligand binding affinities Manually curated and peer-reviewed pathway database with cross-references and visualization tools Structural classifications of proteins deposited in the PDB using a tree-like hierarchy