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HELM was released in 2013, with a single user – Pfizer (who invented it), but were shortly followed by ChemAxon and a steady stream of organisations which represent a wide section of the informatics community. We have also gained recognition from regulators who endorsed HELM as an acceptable format in ISO 11238.
The list of HELM users is now very healthy, and we appreciate our enthusiastic and engaged community. Here are some of the groups who are using HELM.
Wikipedia
We are on Wikipedia! Not sure who added us, but many thanks to whoever it was.
https://en.wikipedia.org/wiki/Hierarchical_Editing_Language_for_Macromolecules
FAIR
HELM has an entry on the FAIR resource https://fairsharing.org/bsg-s001222/ and is pleased to support the initiative to make information Findable, Accessible, Interoperable and Reusable.
Pharma/Biotech
GSK:
GSK is using of the Pistoia Alliance’s Hierarchical Editing Language for Macromolecules (HELM) notation to represent therapeutic large molecules in its bio-registration system, facilitated by the deployment of Dassault Systèmes BIOVIA’s Biological Registration solution. GSK scientists at sites around the world will use the system.
“There is a gap in the space that HELM now covers where there weren’t really any alternatives. It was desirable for GSK to be on a standard rather than create our own notation, and to partner with the Pistoia Alliance and other companies to develop that standard.” Leah O’Brien, Business Consultant, GSK.
Pistoia-Alliance-HELM-GSK-BIOVIA-Case-Study.pdf
Ionis:
Internal registration systems and tools are all based on HELM.
Merck:
Merck has been slowly adopting the HELM notation across our Discovery Chemistry Modalities organization focusing first on simple linear peptides and oligonucleotides. Using the Pistoia HELM editor for creation, editing and registration of monomers and chemical modifiers, our Modalities chemists can now work confidently with their monomers across multiple environments including our biopolymer registration system, our BioviaDraw platform and our tools within Insight for Excel. In 2018 we anticipate incorporating complex, macrocyclic biopolymers into the HELM supported workflows, peptide metabolite identification support and antibody-peptide conjugates. All of this facilitated by the easy to use tools leveraging HELM notation as a foundation.
Novartis:
Novartis makes extensive use of HELM for nucleotide registration and analysis. The open-source HELM tools are integrated with the internal informatics landscape.
Yohann Potier said, “HELM allows Novartis to accurately describe its chemically-modified constructs using an industry standard for registration.”
Pfizer:
As the originators of the HELM standard, Pfizer has based their entire macromolecular registration infrastructure on HELM and its associated biomolecule toolkit.
Sergio Rotstein said, “While the enablement of biomolecular registration was already of great value to Pfizer, the establishment of HELM as an industry standard provided even greater value by facilitating cross-company interoperability and biomolecular data exchange, a very desirable outcome in our increasingly collaborative industry”
Roche:
Starting with HELM Roche has developed the HELM Antibody Editor (HAbE) to enable especially the convenient handling of complex antibody in innovative formats for their analysis, visualization, manipulation and registration.
Most recent is the implementation of HELM2 at Roche to describe, register and manage therapeutic oligonucleotides and their derivates. This was facilitated by the improved monomer handling and support for ambiguous nucleotides within the HELM 2 toolkit.
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Wave:
Merck has been slowly adopting the HELM notation across our Discovery Chemistry Modalities organization focusing first on simple linear peptides and oligonucleotides. Using the Pistoia HELM editor for creation, editing and registration of monomers and chemical modifiers, our Modalities chemists can now work confidently with their monomers across multiple environments including our biopolymer registration system, our BioviaDraw platform and our tools within Insight for Excel. In 2018 we anticipate incorporating complex, macrocyclic biopolymers into the HELM supported workflows, peptide metabolite identification support and antibody-peptide conjugates. All of this facilitated by the easy to use tools leveraging HELM notation as a foundation.
Ionis:
Internal registration systems and tools are all based on HELM.
GSK:
GSK is using of the Pistoia Alliance’s Hierarchical Editing Language for Macromolecules (HELM) notation to represent therapeutic large molecules in its bio-registration system, facilitated by the deployment of Dassault Systèmes BIOVIA’s Biological Registration solution. GSK scientists at sites around the world will use the system.
“There is a gap in the space that HELM now covers where there weren’t really any alternatives. It was desirable for GSK to be on a standard rather than create our own notation, and to partner with the Pistoia Alliance and other companies to develop that standard.” Leah O’Brien, Business Consultant, GSK.
Pistoia-Alliance-HELM-GSK-BIOVIA-Case-Study.pdf
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Wave is in the process of adopting HELM notation for its monomer database and converting all of its registered molecules to the HELM standard. Wave is primarily focused on the oligonucleotide chemistry space, and an interest in defining the use of stereochemistry in phosphorothioate backbone chemistries. The HELM notation is a chemically precise and flexible open source "building block" system that allows us to quickly assemble and render complex molecules and their properties.
Scientific software providers
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