Page Comparison

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• Monomers - the atom/bond representation of the building blocks

• Simple polymers - a linear sequence of monomers of the same type

• Complex polymers - combinations of simple polymers, hydrogen bond information and annotations

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The flexibility allows you to define molecules like this which include a oligonucleotide connected to a small molecule (SMCC) connected to a peptide. 

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HELM1

HELM 2

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. Image Added

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 Image Added

Specification

The HELM 2.04 specification is available below.

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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.

Peptide Monomer Guidelines

We have developed recommendations for creating and naming a monomer set for peptides. 

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Nucleotide Monomer Guidelines

More Information

An academic overview of HELM and its origins

• HELM paper in J.      Chem. Inf. Model.

HELM 1.0 overview

xHELM overview

 HELM 2.0 quick reference diagram

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Notepad++ highlighting definition file

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