The Biomolecule Toolkit is a Web service-based toolkit designed to bridge the gap between biology and chemistry for complex biomolecular entities. It provides unambiguous representation at the sequence and atomic level for a diverse set of biomolecules such as peptides, oligonucleotides, proteins and antibody drug conjugates, including those containing unnatural and chemically-modified components, thereby allowing their storage, indexing and search within a database. The toolkit can be applied to extend existing biologics management platforms or to form the basis of a biomolecule registration system. It is capable of mapping specific workflows and business logic for canonicalization, registration and querying. Under the hood, the toolkit extends the JChem chemistry engine with sequence space and alphanumeric annotations used to define complex modalities, and so enable researchers to easily extend their discovery platforms to also interrogate non-standard biomolecules. The toolkit is available for integration within enterprise research informatics platforms, and development is underway to bring biomolecule support to ChemAxon’s Plexus Suite web collaboration platform and to give bench researchers more reach in the scope of projects supported on the platform.