{"id":512,"date":"2013-05-10T09:05:59","date_gmt":"2013-05-10T08:05:59","guid":{"rendered":"http:\/\/nextmovesoftware.com\/blog\/?p=512"},"modified":"2015-06-22T16:59:08","modified_gmt":"2015-06-22T15:59:08","slug":"handling-biologics-a-perception-problem","status":"publish","type":"post","link":"https:\/\/nextmovesoftware.com\/blog\/2013\/05\/10\/handling-biologics-a-perception-problem\/","title":{"rendered":"Handling biologics: A perception problem?"},"content":{"rendered":"

In an earlier post<\/a>, 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.<\/p>\n

But rather than regarding this as a file format problem, why not consider it instead a perception problem<\/i>. 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.
\n\"Roundtripping\"<\/a>
\nThere 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.<\/p>\n

What I’ve described here and in the previous post<\/a> is the introduction from my ACS presentation on Roundtripping between small-molecule and biopolymer representations<\/b>. This describes the development of the Sugar & Splice<\/a> 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<\/a>.
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