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Pistoia Releases HELM Biomolecular Representation Tools

Published: Tuesday, July 02, 2013
Last Updated: Monday, July 01, 2013
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New software toolkit enables the representation of a wide range of biomolecules (e.g. proteins, nucleotides, antibody drug conjugates)

The Pistoia Alliance has released the HELM biomolecular representation standard software toolkit and editor under the permissive open source MIT license.

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.

The tools include:

- A software toolkit that includes all the functionality needed to implement a HELM-based system.
- A fully functioning macromolecule editor that enables the drawing of macromolecules and generation of HELM notation.

The technology was originally developed at Pfizer and powers their biomolecule registration system and related toolkit.

According to Sergio Rotstein, a Director in Pfizer’s Research Business Technology organization and Domain Lead for the Pistoia Alliance HELM initiative, “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.” He added, “It has been truly inspiring to see how 24 different organizations can come together to deliver so successfully on a joint project. Particularly significant contributions have been made by ChemAxon, Bristol-Myers Squibb, GlaxoSmithKline and Roche.”

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 tbarriers to innovation in life science R&D.”

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