The Pistoia Alliance Hierarchical Editing Language for Macromolecules (HELM) project team is pleased to announce the publication of a curated library of monomers onto GitHub.


Monomers are the building blocks of biomolecules and HELM adopters need to decide what monomers they want to use very early in their journey with HELM. Until now there has been little guidance for monomer set creation and no recommended starting set.


The HELM project team has worked with Evan Bolton of PubChem and Anna Gaulton and Patricia Bento of ChEMBL to analyze their public datasets and identify the monomers that appear most frequently. Using a combination of metrics: the appearance of the monomer in biomolecules in PubChem, ChEMBL, the general literature, and patents, the team has identified a set of just over 300 peptide monomers and nearly 400 nucleotide monomers.


This set is now available on GitHub. Alongside the monomers, we have updated guidelines for creating and naming monomers which are available in our wiki.


We commend these monomers to new users. The set enables you to represent a large number of biomolecules with a tractable number of monomers. As the set becomes established, it is hoped that it will reduce the need for translation of HELM strings from different sources.


For more information on HELM, see


We welcome new members, if you would like to join us please email