The Pistoia Alliance has announced the release of the HELM biomolecular representation standard software toolkit and editor under the permissive open source MIT licence.
The joint project involved an open collaboration between 24 different organisations, highlighting the aim of the Alliance to deliver concepts and pilot projects that support precompetitive collaboration.
HELM (Hierarchical Editing Language for Macromolecules) enables the representation of a wide 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 solves this problem through a hierarchical notation that represents complex macromolecules as polymeric structures with support for unnatural components (e.g. unnatural amino acids) and chemical modifications.
Amongst the 24 different organisations involved in the release of this toolkit, significant contributions were made by ChemAxon, Bristol-Myers Squibb, GlaxoSmithKline and Roche.
The technology was originally developed at Pfizer. Through making this toolkit widely available through an open source licence, the Pistoia Alliance aims to fill an important industry gap, by providing a mechanism for biotherapeutics data exchange within pharma organizations themselves and with their collaborators, something they argue is important in the increasingly externalized world of pharma R&D.
Sergio Rotstein, a Director in Pfizer’s Research Business Technology organization and Domain Lead for the Pistoia Alliance HELM initiative, states, “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, which ultimately benefits everyone.”
John Wise, the Pistoia Alliance’s Executive Director, said, “This is an exciting day for the Pistoia Alliance. Macromolecules are increasingly important as therapeutic agents to treat or palliate human disease. By signposting HELM as the standard of choice for the exchange of macromolecule information in an increasingly externalized R&D environment, and by providing effective tools for groups to work with that standard, the Pistoia Alliance makes another contribution to lowering the barriers to innovation in life science R&D.”