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

HELM attracting attention at Bio-IT World 2015

Having won the 2014 Best Practice Award at the Bio-IT World Conference & Expo, HELM again attracted plenty of attention at this year’s meeting (Boston, April 21-23 2015). Numerous contributions gave an overview of the growing HELM ecosystem and its adoption by the pharmaceutical industry.

HELM Antibody Editor released

The release of the HELM Editor by the Pistoia Alliance in 2014 inspired a team at Roche and quattro research to use this technology for the registration of antibodies engineered at Roche’s research sites.

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 (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.