To represent peptide sequences, the Hierarchidal Editing Language for Macromolecules (HELM) format was used . Compared to the SMILES format , it allows a higher level representation of more complex structures, such as proteins, peptides, oligonucleotides, and small molecules that may be covalently bound. In our context, the HELM format can be used to describe different types of macrocycles, non-natural amino acids or other chemical modifications. To be used as input for the different molecular fingerprint methods and pLMs, peptide sequences represented in HELM format were first converted to SMILES strings and FASTA sequences, respectively.