{"id":428,"date":"2013-04-18T13:50:13","date_gmt":"2013-04-18T12:50:13","guid":{"rendered":"http:\/\/nextmovesoftware.com\/blog\/?p=428"},"modified":"2015-06-22T17:01:01","modified_gmt":"2015-06-22T16:01:01","slug":"handling-biologics-a-file-format-problem","status":"publish","type":"post","link":"https:\/\/nextmovesoftware.com\/blog\/2013\/04\/18\/handling-biologics-a-file-format-problem\/","title":{"rendered":"Handling biologics: A file format problem?"},"content":{"rendered":"

The increasing importance of biological therapeutics, or biologics, to the pharmaceutical industry is well-known. For example, data from Drugs.com<\/a> show that of the top 15 best selling therapies in the US in Q4 2012, six were biologics. Monoclonal antibodies<\/a> are a typical example; these are glycoproteins, comprising of short oligosaccharides attached to a multi-chain polypeptide.<\/p>\n

It is clear that handling such molecules requires a different approach than that taken for small-molecules. For example, here is an all-atom depiction of the peptide crambin<\/a>:
\n\"Crambin\"<\/a>
\nNo – it’s not a cyclic peptide. It just happens to have three disulfide bridges. A more useful depiction can be generated if we follow the IUPAC or FDA guidelines for peptide depiction; here the primary structure is much clearer as is the presence of the disulfide bonds:<\/p>\n

\"FDA\"<\/a>
FDA Style<\/figcaption><\/figure>\n
\"IUPAC\"<\/a>
IUPAC Style<\/figcaption><\/figure>\n

However, to create these sorts of depictions, and otherwise handle biopolymers more appropriately, we need to know the polymer structure.<\/p>\n

Some consider this a file format problem. Some file formats which have been developed to store or represent biopolymer structures include the CHUCKLES<\/a> and CHORTLES<\/a> languages from Chiron and Daylight, HELM<\/a> (Hierarchical Editing Language for Macromolecules) from Pfizer, Protein Line Notation<\/a> from Biochemfusion and SCSR<\/a> (Self-Contained Sequence Representation, an MDL V3000 extension) from Accelrys. Naturally, Wisswesser Line Notation has also been extended<\/a> to handle this problem.<\/p>\n

In particular, the HELM format has recently received support from the Pistoia Alliance<\/a>. See for example this post<\/a> on the Pistoia blog which describes how HELM “gives us a single consistent way to describe macromolecules which can be used across industry and academia” so that “researchers do not have to spend time creating their own notations”.<\/p>\n

But is a new file format the best way to achieve this goal? (I can’t resist inserting the xkcd comic on standards at this point \ud83d\ude42 )<\/p>\n

\"\"
From xkcd, the web comic: http:\/\/xkcd.com\/927\/<\/figcaption><\/figure>\n

While NextMove’s software for handling biopolymers, Sugar & Splice<\/a>, will handle popular file formats such as HELM, I will describe a different view of the problem in the follow-up blog post<\/a>.<\/p>\n","protected":false},"excerpt":{"rendered":"

The increasing importance of biological therapeutics, or biologics, to the pharmaceutical industry is well-known. For example, data from Drugs.com show that of the top 15 best selling therapies in the US in Q4 2012, six were biologics. Monoclonal antibodies are a typical example; these are glycoproteins, comprising of short oligosaccharides attached to a multi-chain polypeptide. … Continue reading Handling biologics: A file format problem?<\/span><\/a><\/p>\n","protected":false},"author":2,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[1],"tags":[],"_links":{"self":[{"href":"https:\/\/nextmovesoftware.com\/blog\/wp-json\/wp\/v2\/posts\/428"}],"collection":[{"href":"https:\/\/nextmovesoftware.com\/blog\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/nextmovesoftware.com\/blog\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/nextmovesoftware.com\/blog\/wp-json\/wp\/v2\/users\/2"}],"replies":[{"embeddable":true,"href":"https:\/\/nextmovesoftware.com\/blog\/wp-json\/wp\/v2\/comments?post=428"}],"version-history":[{"count":34,"href":"https:\/\/nextmovesoftware.com\/blog\/wp-json\/wp\/v2\/posts\/428\/revisions"}],"predecessor-version":[{"id":1460,"href":"https:\/\/nextmovesoftware.com\/blog\/wp-json\/wp\/v2\/posts\/428\/revisions\/1460"}],"wp:attachment":[{"href":"https:\/\/nextmovesoftware.com\/blog\/wp-json\/wp\/v2\/media?parent=428"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/nextmovesoftware.com\/blog\/wp-json\/wp\/v2\/categories?post=428"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/nextmovesoftware.com\/blog\/wp-json\/wp\/v2\/tags?post=428"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}