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.
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.