{"id":1781,"date":"2016-05-26T13:42:29","date_gmt":"2016-05-26T12:42:29","guid":{"rendered":"https:\/\/nextmovesoftware.com\/blog\/?p=1781"},"modified":"2016-05-26T13:42:29","modified_gmt":"2016-05-26T12:42:29","slug":"supporting-the-updated-symbol-nomenclature-for-glycans-snfg","status":"publish","type":"post","link":"https:\/\/nextmovesoftware.com\/blog\/2016\/05\/26\/supporting-the-updated-symbol-nomenclature-for-glycans-snfg\/","title":{"rendered":"Supporting the updated Symbol Nomenclature for Glycans (SNFG)"},"content":{"rendered":"

Even C&EN reported<\/a> the recent standardisation efforts by the oligosaccharide community on symbols to use for glycan* depiction. These guidelines are available online in Appendix 1B<\/a> of Essentials of Glycobiology and will be updated over time.<\/p>\n

As a test case for Sugar & Splice support, I depicted the oligosaccharide below whose structure is strangely reminiscent of Table 1 in the guidelines. For those of you glycan enthusiasts who wish to print T-shirts with this emblazoned on the front, here is an Inkscape-friendly SVG file<\/a>.
\n\"SNFG\"
\nHowever, such a diverse set of monosaccharide symbols is not present in the typical oligosaccharide. I’ve searched PubChem for the entry with the most symbols and found CID91850542<\/a> below with 11. (For an alternative depiction of the same structure, see GlyTouCan<\/a>. Interestingly, the CSDB entry for the same paper describes a different but very similar glycan<\/a>.):
\n\"11_91850542_new\"<\/a><\/p>\n

In fact, having many symbols often indicates a dodgy structure as in the following example (PubChem CID101754793<\/a>) deposited by Nikkaji<\/a> which has 9 monosaccharide symbols. Looking at the original source, the SMILES not only has nitro as [N+](=O)O (must have been corrected by PubChem) but many of the sugars have incorrect stereochemistry (compared to the provided IUPAC name). The D\/L in several of the symbols, indicating the presence of the rarer stereoisomer, is also a red flag.
\n\"09_101754793_new\"<\/a>If you put the IUPAC name through OPSIN<\/a> (after a minor mod), and then depict the resulting SMILES using Sugar & Splice, you get the correct structure:\"tmp\"<\/a><\/p>\n

* Glycans are “compounds consisting of a large number of monosaccharides linked glycosidically”, via Wikipedia and the IUPAC gold book.<\/p>\n","protected":false},"excerpt":{"rendered":"

Even C&EN reported the recent standardisation efforts by the oligosaccharide community on symbols to use for glycan* depiction. These guidelines are available online in Appendix 1B of Essentials of Glycobiology and will be updated over time. As a test case for Sugar & Splice support, I depicted the oligosaccharide below whose structure is strangely reminiscent … Continue reading Supporting the updated Symbol Nomenclature for Glycans (SNFG)<\/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\/1781"}],"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=1781"}],"version-history":[{"count":21,"href":"https:\/\/nextmovesoftware.com\/blog\/wp-json\/wp\/v2\/posts\/1781\/revisions"}],"predecessor-version":[{"id":1806,"href":"https:\/\/nextmovesoftware.com\/blog\/wp-json\/wp\/v2\/posts\/1781\/revisions\/1806"}],"wp:attachment":[{"href":"https:\/\/nextmovesoftware.com\/blog\/wp-json\/wp\/v2\/media?parent=1781"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/nextmovesoftware.com\/blog\/wp-json\/wp\/v2\/categories?post=1781"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/nextmovesoftware.com\/blog\/wp-json\/wp\/v2\/tags?post=1781"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}