What is HELM?

We’ve been talking a lot about HELM (Hierarchical Editing Language for Macromolecules) lately. You may have read about Scilligence’s partnership with Pistoia Alliance and the implementation of HELM features in Scilligence’s JSDraw, TouchMol4Office (including Word, Excel, PowerPoint, OneNote, MedChem Suite), ELN, RegMol, Inventory, and PMF. While we prepare for the official release of the open source HELM editor, we’d like to tell you what HELM is and why you should be excited to use these new features.


HELM’s History

In 2008, Pfizer needed a way to describe complex molecules. Pfizer created HELM’s algorithm and registered their first nucleotide monomers and oligonucleotide therapeutic unit into Pfizer’s database. HELM was born to allow scientists to encode and create a single notation for biomolecules. HELM allows users to edit the structure of ADCs, antibodies, proteins, peptides, and nucleotides.

Simultaneously, researchers from a number of life science companies, including Pfizer, joined together to create Pistoia Alliance, a not-for-profit alliance whose goal was to solve the inconsistencies that exist in life science R&D and quicken the path to innovation in the field.

As part of their mission to provide innovative R&D technologies to the community, Pistoia Alliance decided to make Pfizer’s HELM completely free to the public. HELM had been previously developed for Pfizer’s use internally so an open source HELM editor needed to be developed. Being impressed with Scilligence’s technology, Pistoia chose Scilligence to develop the new web-editor, which will be released in the next few months.


How Does HELM Work?

Picture by Pistoia Alliance depicts a complex oligonucleotide peptide conjugate, amino acids, RNA, and other chemical structures in a monomer graph (top) and HELM notation (bottom).

HELM uses hierarchical levels to encode structures. Monomers are given unique identifiers that are strung together to create sequences. These sequences can be connected and contain multiple sequence types. The IDs are linked to a complete description in small molecule notation. 1


Why is HELM Important?

Before HELM, there was no way for scientists to depict complex biomolecules. HELM creates a standard for representing, exchanging, and manipulating complex molecular entities thus, improving data storage and transfer and knowledge sharing in research.

For more details about HELM: openhelm.org


1 Details of how HELM works 

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