The registration of peptide and peptide-like structures in chemical databases poses a number of technical challenges, as do other biological oligomers.  Primary among these are the size and complexity of these compounds, often making it difficult or impossible for a biochemist to identify differences or similarities between compounds stored as all-atom representations.  For biological (proteinogenic) sequences the solution is simple, to use strings of the one (or three) letter codes to represent the biopolymer.  However, for post-translationally modified, D-, cyclic and non-standard peptides the way forward is less clear.  One approach is to use an ever larger dictionary three letter codes to encode common non-standard amino acids.  Unfortunately, this method quickly becomes unwieldy once the set of abbreviations exceeds those frequently encountered in the literature, requiring a chemist to consult a key or dictionary for entry or interpretation of structures.  In this presentation, we propose the use of semi-systematic monomer names, based upon readily recognizable chemical line formulae, for the encoding and display of traditionally difficult to handle peptides.  These rules lead to names such as N(Me)Ser(tBuOH) that are similar to those seen/used in scientific publications, though not formally ratified by IUPAC nor CAS.

Representation and display of non-standard peptides using semi-systematic amino acid monomer naming

247th National Meeting (2014)

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