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.
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.
Internal registration systems and tools are all based on HELM.
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 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.”
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”
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.
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
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 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.
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.