HELM

Provides support for HELM notation (Hierarchical Editing Language for Macromolecules) - a single notation that can encode the structure of complex biomolecules including diverse polymers, non-natural monomers and complex attachment points.

Andrew Skalkin | issue tracker | beta

Features

• Automatic detection of HELM values in datasets
• Rendering in the spreadsheet
• Editing
• Conversion to SMARTS and MOLBLOCK
• Substructure search
• Similarity search
• Calculators (mol weight, mol formula, extinction coefficient, )
• Data augmentation (show relevant information in the context panel)

Advanced features

• Integration with the HELM2WebService (calculations, images, etc)
• Support for company-specific monomer libraries
• Management tool for monomer libraries (integrated with the security and privileges)
• Similarity and diversity analyses
• HELM space (UMAP or t-SNE based on the distance)
• Activity cliffs analysis (based on the HELM space)

Kudos to Pistoia alliance for open-sourcing the HELM Web Editor that is used in this integration.

See also:

• https://pistoiaalliance.atlassian.net/wiki/spaces/HELM/overview
• https://github.com/PistoiaHELM/HELMWebEditor