NON-NATURAL AMINO ACID NOMENCLATURE FOR HELM MONOMER REGISTRATION

The growing interest in studying modified and cyclic peptides is constrained by limitations in how their chemical information is encoded, represented, and analysed. Traditional sequence formats such as FASTA only allow working with linear and natural peptides. HELM and BILN formats provide more versatile and extendible notation systems for the representation of peptides with nonnatural monomers or cyclic arrangements. HELM is a notation that uses a database as a source of monomers where these are defined on their structure, identifier, and attachment points. While structural representations are canonicalized using established methods, there is currently no widely accepted convention for naming peptide monomers. In this manuscript, we develop on top of the guidelines proposed by Pistoia Alliance for the naming of non-natural amino acids for their representation using HELM. Our nomenclature extends on modifications of side chains and backbone, naming of homo amino acids and peptoids, and resolves ambiguous cases using a combination of systematic and pragmatic rules.