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Pistoia Alliance Releases Open Source Language for Representing Complex Biomolecules


This week, the Pistoia Alliance released the Hierarchical Editing Language for Macromolecules, or HELM, an open source software toolkit and editor for representing complex biomolecules such as proteins, nucleotides, antibody drug conjugates.

The newly launched toolkit provides all the functionality needed to implement a HELM-based system and an editor that lets users draw macromolecules and calculate molecular properties.

HELM, which was originally developed by Pfizer, provides a way to represent molecules that are too large to represent atomically or which contain non-natural chemical modifications that make it impractical to represent them as sequences.

HELM's structure hierarchy consists of complex and simple polymers, monomers, and atoms. It describes monomers using atoms and bonds, single-type polymers are described as a sequence of monomers, and complex multi-type polymers are described as connected polymers.

A detailed description of HELM is available in a paper that was published in the Journal of Chemical Information and Modeling.

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