PubChem, as the standard bearer for online chemical databases, has long been the deposition site of choice for chemical data. In addition to this, it also contains a wealth of information on biologics, as oligosaccharides, oligopeptides and oligonucleotides are essentially medium to large chemicals. Recent years have seen direct depositions of biologic databases into PubChem, in addition to their appearance in vendor catalogs. Biologics are typically represented using a reduced graph notation, where the constituent monomers are represented by a short name or indeed a single letter, whereas a small molecules uses an all-atom representation. Our system can interconvert between these representations thus enabling a biologics lens on existing chemical data. Here we describe an analysis of the biologics contained in PubChem, using information publicly available from PubChem under the term “Biologic Description”. Using the biologics subset of PubChem, we will look at the distribution of non-standard amino acids and attached substituents, and investigate questions such as how many knottins are present, are different disulfide bridging architectures present for the same peptide, and how the use of a reference database of named peptides (derived from vendor catalogs, ChEBI, Wikipedia, UniProt, for example) can be leveraged to name peptides as derivatives of the reference entries. We also consider possible ways of searching these data from grepping the IUPAC condensed representation to more sophisticated methods similar to SMARTS on the underlying data structure.

PubChem as a biologics database

254th National Meeting (2017)

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