Compound or Compound-Specific Databases

• PubChem
  PubChem is a freely available database of chemical structures of small organic molecules and information on their biological activities. It contains structure, nomenclature and calculated physico-chemical data and is linked with NIH PubMed/Entrez information. PubChem is organized as three linked databases within the NCBI's Entrez information retrieval system. These are PubChem Substance, PubChem Compound, and PubChem BioAssay. PubChem also provides a fast chemical structure similarity search tool. PubChem has >19 million unique chemical structures.
• ChEBI
  Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on 'small' chemical compounds. The chemical entities in ChEBI are either products of nature (metabolites) or synthetic products used to intervene in the processes of living organisms (drugs or toxins). ChEBI contains structure and nomenclature information along with hyperlinks to many well-regarded databases.  ChEBI uses a carefully developed ontological classification, whereby the relationships between molecular entities or classes of entities and their parents and/or children are precisely specified.  ChEBI has >15,500 chemical entities in its database.
• ChemSpider
  ChemSpider is an aggregated database of organic molecules containing more than 20 million compounds from many different providers. At present the database contains information from such diverse sources as a marine natural products database, ACD-Labs chemical databases, the EPA's DSSTox databases and from a series of chemical vendors. It has extensive search utilities and most compounds have a large number of calculated physico-chemical property values.
• KEGG Glycan
  The KEGG GLYCAN database is a collection of experimentally determined glycan structures. It contains all unique structures taken from CarbBank, structures entered from recent publications, and structures present in KEGG pathways.  KEGG Glycan has >11,000 glycan structures from a large number of eukaryotic and prokaryotic sources.

Drug Databases

• DrugBank
  The DrugBank database is a blended bioinformatics and cheminformatics resource 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 nearly 4800 drug entries including >1,350 FDA-approved small molecule drugs, 123 FDA-approved biotech (protein/peptide) drugs, 71 nutraceuticals and >3,243 experimental drugs.  DrugBank also contains extensive SNP-drug data that is useful for pharmacogenomics studies.
• Therapeutic Target Database
  The Therapeutic Target Database (TTD) is a drug database designed to provide information about the known therapeutic protein and nucleic acid targets described in the literature, the targeted disease conditions, the pathway information and the corresponding drugs/ligands directed at each of these targets. The database currently contains 1535 targets and 2107 drugs/ligands.
• PharmGKB
  The PharmGKB database is a central repository for genetic, genomic, molecular and cellular phenotype data and clinical information about people who have participated in pharmacogenomics research studies. The data includes, but is not limited to, clinical and basic pharmacokinetic and pharmacogenomic research in the cardiovascular, pulmonary, cancer, pathways, metabolic and transporter domains. Its aim is to aid researchers in understanding how genetic variation among individuals contributes to differences in reactions to drugs.  PharmGKB contains searchable data on genes (>20,000), diseases (>3000), drugs (>2500) and pathways (53). It also has detailed information on 470 genetic variants (SNP data) affecting drug metabolism.
• STITCH
  STITCH ('search tool for interactions of chemicals') is a searchable database that integrates information about interactions from metabolic pathways, crystal structures, binding experiments and drug-target relationships. Text mining and chemical structure similarity is used to predict relations between chemicals. Each proposed interaction can be traced back to the original data sources. The database contains interaction information for over 68 000 different chemicals, including 2200 drugs, and connects them to 1.5 million genes across 373 genomes.
• SuperTarget
  SuperTarget is a database that contains a core dataset of about 7300 drug-target relations of which 4900 interactions have been subjected to a more extensive manual annotation effort.  SuperTarget provides tools for 2D drug screening and sequence comparison of the targets. The database contains more than 2500 target proteins, which are annotated with about 7300 relations to 1500 drugs; the vast majority of entries have pointers to the respective literature source. A subset of 775 more extensively annotated drugs is provided separately through the Matador database (Manually Annotated Targets And Drugs Online Resource).

Spectral Databases

• HMDB
  The Human Metabolome Database (HMDB) is a freely available electronic database containing detailed information about small molecule metabolites found in the human body.  It contains experimental MS/MS data for 800 compounds, experimental 1H and 13C NMR data (and assignments) for 790 compounds and GC/MS spectral and retention index data for 260 compounds.  Additionally, predicted 1H and 13C NMR spectra have been generated for 3100 compounds.  All spectral databases are downloadable and searchable.
• BMRB
  The BioMagResBank (BMRB) is the central repository for experimental NMR spectral data, primarily for macromolecules.  The BMRB also contains a recently established subsection for metabolite data.  The current metabolomics database contains structures, structure viewing applets, nomenclature data, extensive 1D and 2D spectral peak lists (from 1D, TOCSY, DEPT, HSQC experiments), raw spectra and FIDs for nearly 500 molecules.  The data is both searchable and downloadable.
• MMCD
  The Madison Metabolomics Consortium Database (MMCD) is a database on small molecules of biological interest gathered from electronic databases and the scientific literature. It contains approximately 10,000 metabolite entries and experimental spectral data on about 500 compounds.  Each metabolite entry in the MMCD is supported by information in an average of 50 separate data fields, which provide the chemical formula, names and synonyms, structure, physical and chemical properties, NMR and MS data on pure compounds under defined conditions where available, NMR chemical shifts determined by empirical and/or theoretical approaches, information on the presence of the metabolite in different biological species, and extensive links to images, references, and other public databases.
• MassBank
  MassBank is a mass spectral database of experimentally acquired high resolution MS spectra of metabolites.  Maintained and supported by he JST-BIRD project, it offers various query methods for standard spectra obtained from Keio University, RIKEN PSC, and other Japanese research institutions.  It is officially sanctioned bythe Mass Spectrometry Society of Japan.  The database has very detailed MS data and excellent spectral/structure searching utilities.  More than 13,000 spectra from 1900 different compounds are available.
• Golm Metabolome Database
  The Golm Metabolome Database provides public access to custom GC/MS libraries which are stored as Mass Spectral (MS) and Retention Time Index (RI) Libraries (MSRI). These libraries of mass spectral and retention time indices can be used with the NIST/AMDIS software to identify metabolites according their spectral tags and RI's.  The libraries are both searchable and downloadable and have been carefully collected under defined conditions on several types of GC/MS instruments (quadrupole and TOF).
• Metlin
  The METLIN Metabolite Database is a repository for mass spectral metabolite data. All metabolites are neutral or free acids. It is a collaborative effort between the Siuzdak and Abagyan groups and Center for Mass Spectrometry at The Scripps Research Institute.  METLIN is searchable by compound name, mass, formula or structure.  It contains 15,000 structures, including more than 8000 di and tripeptides.  METLIN contains MS/MS, LC/MS and FTMS data that can be searched by peak lists, mass range, biological source or disease.
• Fiehn GC-MS Database
  This library contains data on 713 compounds (name, structure, CAS ID, other links) for which GC/MS data (spectra and retention indices) have been collected by the Fiehn laboratory.  A locally maintain program called BinBase/Bellerophon filters input GC/MS spectra and uses the spectral library to identify compounds.  The actual GC/MS library is available from several different GC/MS vendors.
• BML-NMR
  The Birmingham Metabolite Library Nuclear Magnetic Resonance database is a freely available resource containing 3328 NMR spectra of 208 common metabolite standards. This database includes both 2-D 1H J-resolved spectra and 1-D 1H spectra, recorded at 500 MHz using various water suppression methods and acquisition parameters, for solutions at pH values of 6.6, 7.0 and 7.4. The raw and processed data, including associated metadata, are housed in a purpose-built MySQL database that is compliant with the Metabolomics Standards Initiative (MSI) endorsed reporting requirements, with some necessary amendments. Library data can be accessed freely and searched through a custom written web interface. FIDs, NMR spectra and associated metadata can be downloaded according to a newly implemented MSI-compatible XML schema.

Disease & Physiology Databases

• OMIM
  Online Mendelian Inheritance in Man (OMIM) is a comprehensive compendium of human genes and genetic phenotypes. The full-text, referenced overviews in OMIM contain information on all known Mendelian disorders and over 12,000 genes. OMIM focuses on the relationship between phenotype and genotype. It is updated daily, and the entries contain many links to other genetics resources.  OMIM contains 379 diseases with associated gene sequence data as well as 2385 conditions with a disease phenotype and a known genetic cause.
• METAGENE
  METAGENE is a knowledgebase for inborn errors of metabolism providing information about the disease, genetic cause, treatment and the characteristic metabolite concentrations or clinical tests that may be used to diagnose or monitor the condition.  It has data on 431 genetic diseases.
• OMMBID
  OMMBID or the On-Line Metabolic and Molecular Basis to Inherited Disease is an web-accessible book/encyclopedia describing the genetics, metabolism, diagnosis and treatment of hundreds of metabolic disorders contributed from hundreds of experts.  It also contains extensive reviews, detailed pathways, chemical structures, physiological data and tables that are particularly useful for clinical biochemists.  Most university libraries have subscriptions to this resource.  OMMBID was originally developed by Charles Scriver at McGill.