Global nonprofit Pistoia Alliance released the HELM (Hierarchical Editing Language for Macromolecules) biomolecular representation standard software toolkit and editor under the permissive open source MIT license.
HELM enables the representation of a 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 addresses this issue through a hierarchical notation that represents complex macromolecules as polymeric structures with support for unnatural components (e.g. unnatural amino acids) and chemical modifications.
The technology was originally developed at Pfizer and powers its biomolecule registration system and related toolkit.
"When we started presenting HELM outside of Pfizer, it became obvious that many companies across the industry were facing the same challenges we had faced. By sharing this work in a pre-competitive fashion through the Pistoia Alliance, we are not only helping others to solve this problem but also fostering a technical means by which companies, institutes, CROs, software vendors and IT service providers can exchange biomolecule data and information," said Sergio Rotstein, a director at Pfizer and domain lead for the Pistoia Alliance HELM initiative.