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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.
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.”
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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
We are grateful to all funders, including the above plus BMSWave 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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ACD/Labs supports HELM across our portfolio, from the ACD/Labs Biosequence tool (ACD/ChemSketch) to our array of software for analytical chemistry ACD/Spectrus, and the Luminata CMC project decision support application, to the recently announced Katalyst D2D for high throughput and parallel experimentation. Notations for biomolecules ranging from small peptides to whole antibodies can be imported from HELM and xHELM files and exported in HELM file format. “HELM notation is the cornerstone of our expanded molecular characterization efforts, from small molecule to biologics”,- says CEO Daria Thorp.
Benchling
Benchling supports chemically modified oligonucleotide design, analysis, and characterization in a high-throughput manner using HELM notation. By standardizing on HELM in a single platform, R&D teams can centralize experimental results, standardize oligo sequences and naming uniqueness during registration, and collaborate with teammates more effectively. HELM allows scientists using Benchling to establish a scalable common language across organizations, improve data quality, surface real-time scientific insights, and accelerate the speed of the full therapeutic lifecycle. Benchling users can also interconvert ITD syntax to HELM sequences making it easier to share designed sequences with vendors and collaborators.
Biovia:
Applications use Biovia’s proprietary SCSR (Self-Contained Sequence representation, an extension of the V3000 molfile) format, but there is extensive ability to import, export and convert to and from HELM. Pipeline Pilot Chemistry Collection contains importers and exporters, HELM readers and writers including XHELM, and components to interconvert between macromolecules represented by HELM, full chemistry and SCSR. HELM support is available in Insight, the Draw and Pipette sketchers, biological registration and the chemistry cartridge.
Certara:
Certara’s D360 application for scientific informatics supports discovery research scientists through self-service access data access, integrated analysis and data visualization capabilities combined with collaboration tools to improve data driven decision making. D360 has been deployed in support of small molecule and research into other modalities such as antibodies, ADCs, oligonucleotides, and peptides. D360 supports the use of HELM notation for searching, filtering and rendering other modalities. More advanced functionality, such as sequence formatting, alignment and clustering based on HELM representation allows users to determine and exploit sequence-activity relationships.
ChemAxon:
Biomolecule Toolkit and the macromolecule sketcher BioEddie are natively supporting the HELM standard. The tools provide capabilities for managing a centralized monomer library, registering and performing uniqueness checks of macromolecules, generating a HELM notation from small molecule representations and sequences, and representing modalities with partially or fully unknown chemical structures.
Roland Knispel, Project Lead for Biologics Informatics at ChemAxon, said, “Our HELM-based tools are helping our customers to manage chemically modified sequence-based modalities. A single environment for various types of modalities, improved data quality and utilizing an industry-wide standard for data exchange are the key benefits reported back to us by our users. By market demand our platform is now being integrated into solutions provided by IDBS and other partners.”
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