MOLECULAR MODELLING

HELM

25 June 2013

Pistoia Alliance

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

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 released include a software toolkit that includes all the functionality needed to implement a HELM-based system and 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.

Sergio Rotstein, a director of Pfizer’s research business technology organisation, said: '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.'

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