Biomolecule Toolkit

Merging chemistry and biomolecules

The Biomolecule Toolkit enables standardization, storage and search with a wide range of biological modalities. From fully characterized, to fully unknown; the toolkit provides a data management platform for Biologics from early discovery to late stage development - By unambiguously representing all currently available information about: chemical structures, sequences, components, stoichiometry, annotations and genealogic relationships.
Biomolecule Toolkit and BioEddie: is your equivalent for JChem Engines and Marvin for the Biologics world.
Available in:

Supported types of Biologics

The Biomolecule Toolkit supports a diverse set of biological modalities such as peptides, oligonucleotides, proteins, antibodies, antibody drug conjugates, nanoparticle conjugates, including those containing non-natural or chemically modified residues and chemical decorations. Any of the above may be represented with full, partial, or no chemical structure information or added annotations. All other biological assets such as cell lines, plasmids, pooled samples, and clones are represented by their relevant metadata and annotations.


Use cases

Dumping proteins into your small molecule databases? Are chemical derivatives of peptide and nucleic acid sequences your daily business? In need of support for a novel type of chemistry with an ever more complex and exotic composition? Looking to consolidate numerous registration systems each tailored to a single entity type? Are you seeing your workflow accumulate “incomplete” substance descriptions at terrifying speed?

If you answered 'yes' to any of the above, you should be considering the Biomolecule Toolkit - A rich stack covering all your needs for the representation of any: biological entity class, standardization, registration according to your preferred business logic, file format conversions, property calculations, and comprehensive searching in sequence, chemical structure and annotation space. Soon arriving in Instant JChem, Plexus Suite and other applications near you!

Antibodies represented in Biomolecule Toolkit

Platform Toolkit

With native support of MOL, FASTA and HELM file formats and full interconversion capability between those, the Biomolecule Toolkit is well-suited as either - a core backend for full stack management of biological modalities, or as a modular extension to existing bioinformatics or cheminformatics suite of tools. The Biomolecule Toolkit ships with a JAVA and a REST-ful web service API for easy integration and is the first commercially available toolkit supporting the HELM standard.

Architecture of Biomolecule Toolkit


Training & Examples
Support & FAQ