Handling biologics: A perception problem?

In an earlier post, I described the importance of knowing the biopolymer structure when handling biologics. I also discussed various file formats that have been proposed to address this.

But rather than regarding this as a file format problem, why not consider it instead a perception problem. If we can perceive the biopolymer structure from an all-atom representation, then interconverting between any file format (whether one of the proposed biopolymer formats or existing all-atom representations such as SMILES) is straightforward. Can it be done? Well, that’s what exactly what PDB file writers do; they perceive the amino acid sequence from the all-atom structure and fill in the relevant columns in the PDB file.
There are several benefits to this approach. To begin with, it avoids the cost associated with a new registry system based on a macromolecular file format. There are no problems with new and unusual monomers; these will be faithfully stored in the all-atom representation. The de-facto standards for chemical information interchange, SMILES and MOL files, can be used as always for exchange of data. Tools for small-molecule analysis (e.g. SMARTS searching) can be combined with analyses based on biopolymer structure (e.g. HELM depiction, Smith-Waterman searching). And finally it’s worth considering that it may be difficult to migrate at a later date if a registry system is based on a particular file format.

What I’ve described here and in the previous post is the introduction from my ACS presentation on Roundtripping between small-molecule and biopolymer representations. This describes the development of the Sugar & Splice software for handling oligopeptides, oligonucleotides and oligosaccharides (including modified residues and mixtures of different biopolymers). Note that the presentation is somewhat sugar-centric; for more info on the peptide and nucleotide side of things see Roger’s Spring 2012 ACS presentation.

(For more presentations from NextMove Software, see our SlideShare page.)

One thought on “Handling biologics: A perception problem?”

Leave a Reply

Your email address will not be published.

This site uses Akismet to reduce spam. Learn how your comment data is processed.