Annotations and how to use them

Annotations can be added to HELM strings in two main ways.

In-line annotations

In-line annotations are added in the first section and apply to the element that immediately proceeds them. These annotations are simple text and useful to add descriptions to specific parts of the molecule. 


  • PEPTIDE1{A.A.C"mutation".D.E.E}$$$$




  • CHEM1{[SMCC]}|PEPTIDE1{A.A.A.C.D.D.E.E}$PEPTIDE1,CHEM1,C:R3-1:R1"Specific Conjugation"$$$V2.0

Third section annotations

These annotations are designed to hold more complex information and can contain any valid JSON. This allows for a wide variety of very precise information to be added to the molecule, but all of it relates to the molecule as a whole. 

  • BLOB1{Bead}$$${"Name":"Gold particle conjugated with peptides","Load":26}$V2.0

We would like to work on defining conventions for commonly used information. Please contact the team if you have any suggestions as we are very interested in getting people together to define best practice. 


If you want to add a title to your HELM molecule we recommend using the annotation (third) section of the HELM string to do this. 

  • PEPTIDE1{H.E.L.M}$$${“PEPTIDE1”:{“Title”:”MyTitle”}}$V2.0 

You should not add titles to the end of a HELM string like this:

PEPTIDE1{H.E.L.M}$$$$V2.0 MyTitle.