Find out how HELM can transform your storage of molecule information

HELM Editor

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Open Source Project

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Specifications, user guides & slide sets

Recent HELM Updates

ChEMBL 20 takes the HELM

ChEMBL 20 incorporates the Hierarchical Editing Language for Macromolecules (HELM), the macromolecular representation standard recently released by the Pistoia Alliance.

ChemAxon Biomolecule Toolkit includes HELM compatibility

ChemAxon, a Pistoia Alliance member, has today released its new Biomolecule Toolkit product. The Biomolecule Toolkit includes HELM compatibility making it fully interoperable with an increasing number of other HELM-aware solutions and adopters.

HELM Phase 1 Exceeded Expectations

The Pistoia Alliance HELM project started almost two years ago in December 2012 when David Klatte proposed that the Pistoia Alliance help open source a technology first developed for internal use at Pfizer. That technology was HELM and it enabled the representation of complex macromolecules. The Pistoia Alliance membership enthusiastically embraced the idea and the HELM project was born.

HELM takes on indescribable biology

HELM addresses a problem at the root level of drug discovery. Pharmaceutical and biotech companies are looking at increasingly complex molecules in the search for new therapeutics, testing out RNA- and peptide-based compounds that tap directly into cellular pathways.


HELM (Hierarchical Editing Language for Macromolecules) enables the representation of a wide range of biomolecules (e.g. proteins, nucleotides, antibody drug conjugates) whose size and complexity render existing small-molecule and sequence-based informatics methodologies impractical or unusable.

HELM allows you to build the molecule at a number of levels, this means you can also view and manipulate the structure at those levels. It is a notation, a reference implementation available as code and compiled software, and a community dedicated to extending and managing HELM. We love to have new members, so please get in touch and get involved.

Currently the following companies are involved in the community:


HELM was first conceived at Pfizer in the summer of 2008 to support the Pfizer oligonucleotide therapeutic unit and molecules were first registered into the Pfizer corporate database using HELM in December 2008. Since then work has continued on a sophisticated molecule editor known as PME and the registration tool known as PMR. In December 20012 the Pistoia Alliance inaugurated a project to publish the notation and externalise the Pfizer code, and thus make HELM available free to all who would like to use it. This website has been created by that project and contains the output so far. We are continuing work, so please check back regularly for updates.

Contact the HELM Team

There are quite a few ways to participate in the HELM project and community, and not all of them involve contributing code. Participating in discussions, or filing bug reports or enhancement requests are incredibly valuable forms of participation. We also need people who can write documentation and help us publicise what we are doing. Please get involved – we would love to hear from you!

Access the HELM GitHub repsitory

The source code for all HELM components can be found in our GitHub repository.