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The Hierarchical Editing Language for Macromolecules was designed to create a single notation that can encode the structure of complex biomolecules including diverse polymers, non-natural monomers and complex attachment points.


HELM was first conceived at Pfizer in the summer of 2008 to support the Pfizer oligonucleotide therapeutic unit and molecules were first registered into the Pfizer corporate database using HELM in December 2008.

HELM: A Hierarchical Notation Language for Complex Biomolecule Structure Representation Tianhong Zhang, Hongli Li, Hualin Xi, Robert V. Stanton, and Sergio H. RotsteinJournal of Chemical Information and Modeling 2012 52 (10), 2796-2806DOI: 10.1021/ci3001925

How it works

HELM contains multiple levels of information:


There are 2 major releases of HELM.



Covers different types of macromolecule : DNA/RNA, PEPTIDE and CHEM polymer types

Allows non-natural monomers : Monomers are defined by the HELM author, so there is no limit on the monomers that can be included in your molecule.

Is portable

xHELM allows you to ‘bundle’ all the monomer information with your molecule definition into a single package that can be used to transfer information outside your organisation.

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Adds the ability to define 

  • Unknown sections of or entire polymers

  • Repeating units

  • Annotations

  • Unknown connection points

  • Multiple possible connection points

  • Probabilities of different monomers or polymers

  • Mixtures

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The HELM 2.04 specification is available below.