HELM is dependent on monomer definitions and the curation of the monomer set used is critical.
The HELM team developed the HELMCoreLibrary using frequency analysis of public datasets in collaboration with the EBI and PubChem. The principles and naming conventions used are documented below. We would recommend adopting HELMCoreLibrary wherever possible and ensuring that you conform to these recommendations if you develop your own monomers.
Peptide Monomer Guidelines
Nucleotide Monomer Naming