Existing cheminformatics toolkits provide a mature set of tools to handle small-molecule data, from generating depictions, to creating and reading linear representations (such as SMILES and InChI).  However, such tools do not translate well to the domain of biopolymers where the key information is the identity of the repeating unit and the nature of the connections between them. For example, a typical all-atom 2D depiction of all but the smallest protein or oligosaccharide obscures this key structural information. We describe a suite of tools which allow seamless interconversion between appropriate structure representations for small molecules and biopolymers (with a focus on polypeptides and oligosaccharides). For example:SMILES: OC[C@H]1O[C@@H](O[C@@H]2[C@@H](CO)OC([C@@H]([C@H]2O)NC(=O)C)O)[C@@H]([C@H]([C@H]1O)O[C@@]1(C[C@H](O)[C@H]([C@@H](O1)[C@@H]([C@@H](CO)O)O)NC(=O)C)C(=O)O)OShortened IUPAC format: NeuAc(a2-3)Gal(b1-4)GlcNAc I will discuss the challenge of supporting a variety of biopolymer representations, handling chemically-modified structures, and handling biopolymers with unknown attachment points (e.g. from mass spectrometry).

Roundtripping between small-molecule and biopolymer representations

245th National Meeting (2013)

The official archive and repository for all ACS Meetings & Expositions abstracts and select posters or presentations.