ChEBI (Chemical Entities of Biological Interest) is a dictionary of small molecular entities. It is manually annotated and provides a chemical ontology to describe small molecules, including their biological and chemical roles.

ChEMBL is a database of bioactive compounds that focuses on interactions between small molecules and their macromolecular targets, including medicinal chemistry, clinical development and therapeutics data.

The Enzyme Portal integrates publicly available information from the UniProt Knowledgebase, the Protein Data Bank in Europe, Rhea, Reactome, IntEnz, ChEBI, ChEMBL, Cofactor and MACiE.

Integrated Database of Small Molecules.
Aggregating many different sources of information about small molecules into a single, logically coherent and semantically interconnected information source.

A curated database of drug targets, prescription medicines and experimental drugs.

Analysis of raw GC- and LC-MS metabolome data against the either the GMD database or user defined libraries in NIST.

MetaboLights is a database for metabolomics experiments and derived information. 

Automated inference of elemental fluxes in microbial communities, now integrated as TOPP into OpenMS

Mass Spec. analysis platform

(See also Topp, LFQProfiler & RNPxl, MetaboProfiler) 

Importing and analysing Mass Spec. data in a range of formats and for protein identification.
 

SugarBind covers knowledge of glycan binding of human pathogen lectins and adhesins. Information is collected by experts from articles published in peer-reviewed scientific journals.

A knowledge resource for lipids and their biology.