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September 15, 2013 (Vol. 33 , No. 16)

Open-Source Tools for Representing Macromolecules

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Pistoia Alliance

The Hierarchical Editing Language for Macromolecules (HELM) enables the representation of a range of biomolecules (such as proteins, nucleotides, and antibody-drug conjugates) whose size and complexity render existing small molecule and sequence-based informatics methodologies impractical or unusable. HELM works through a hierarchical notation that represents complex macromolecules as polymeric structures with support for unnatural components (such as unnatural amino acids) and chemical modifications. HELM technology, originally developed by Pfizer, is being shared via open-source tools—a software toolkit that includes the functionality needed to implement a HELM-based system, as well as a macromolecule editor that enables the drawing of macromolecules and generation of HELM notation.

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