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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.
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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.
How it works
HELM contains multiple levels of information:
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There are 2 major releases of HELM.
HELM1 | HELM 2 |
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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. | Adds the ability to define
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Specification
The HELM 2.04 specification is available below.
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Added links to the monomer JSON schema.
Added location of xml schema for xHELM.
Clarified mandatory use of ? for connection points with unknown monomers like *, X and N.
Clarified rules for the use of in-line HELM particularly around connection point definition.
Minor revisions to aid clarity.
HELM Test set
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The team have compiled a set of around 150 structures that illustrate the full range of structures that can be encoded in HELM.This is included as a resource for anyone who wants to implement their own HELM tools rather than use the open source toolkit.
HELM Examples from ChEMBL
Roger Sayle kindly created this file of 1000 (inline) HELM strings from ChEMBL 21.It includes examples of multiple peptide chains, and nucleic acid sequences, but doesn't cover all of the corners of the HELM v2 (or v1.1) specification. It was created using the monomerlib2 monomer set.
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Notepad++ highlighting definition file
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