HELM notation

For small molecules, there exists a number of formats for the representation of chemical structures such as SMILES, InChi etc. However, the hierarchical structure of complex biomolecules is challenging to represent in a concise notation. Here it comes to HELM notation, a single notation that can encode the structure of complex biomolecules including diverse polymers, non-natural monomers and complex attachment points.

And we are ready to announce Helm support on Datagrok platform with Helm package, built on HELMWebEditor and HELM2WebService created by Pistoia Alliance.

Helm package enables such features as:

  • Automatic detection of HELM values in datasets
  • Rendering in the spreadsheet
  • Editing in HelmWebEditor
  • Conversion to SMILES and MOLBLOCK
  • Calculators (mol weight, mol formula, extinction coefficient)
  • Integration with the HELM2WebService (calculations, images, etc)
  • Support for company-specific monomer libraries

Let’s take a look at how the HelmWebEditor works.

The example of uploading monomer library is presented below.

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