CAZypedia:Community Portal

Please write your ideas/suggestions/etc. for the improvement of CAZypedia on this page. Community participation is essential for the continued development of this resource!

PLEASE NOTE: If you leave a comment here, please sign it by adding four tildes (~~~~) after your post. Thanks! Harry Brumer 05:21, 29 July 2009 (CEST)

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Nomenclature of sugar ring faces

• Confusion about sugar ring faces; GH people seem to prefer calling the faces based on the sides relative to the anomeric carbon (C1), but lectin (or sugar-binding protein) people usually call them according to a definition of faces of ring compounds (PMID: 16592816). They are unfortunately "upside down" (D. Ross). ShinyaFushinobu 07:06, 31 August 2009 (UTC)
  • Thanks for the comment. I've passed this on to User:Steve Withers and User:Spencer Williams, who are maintaining the lexicon for their comments. Harry Brumer 07:45, 31 August 2009 (UTC)
  • Dear Shinya, the nomenclature of Wimmer et al. works well for many compound classes, but has limitations with sugars. In particular, there is potential conflict with the use of the terms alpha and beta, which for carbohydrates is used for the anomeric configuration. When using the Wimmer nomenclature, for D-sugars the alpha face is the same as that which the alpha anomeric substituent is oriented. However, for L-sugars, the nomenclature for faces and the anomeric orientations are opposed. I appreciate that different communities have different 'lexicons'; in the case of GHs teh anomeric configuration is frequently discussed in close concert with the face of the molecule and so the use of the anomeric configuration to define faces would appear more convenient. As a point of interest - do you happen to know whether IUPAC or IUBMB has adopted a formal definition of the face of a molecule? The closest I have seen for sugars is the top and bottom faces defined in the "CONFORMATIONAL NOMENCLATURE FOR FIVE- AND SIX-MEMBERED RING FORMS OF MONOSACCHARIDES AND THEIR DERIVATIVES (Pure & Appi. Chem., 1981, Vol.53, pp.1901—1905).Spencer Williams 12:07, 31 August 2009 (UTC)

I must confess I was not aware of this other nomenclature.. Personally I do not see that we can use other than the IUPAC carbohydrate nomenclature or all hell would break loose. However, perhaps when the CBM section is included we should make a note there about the lectin nomenclature (or even now in the Lexicon).Steve Withers 14:28, 31 August 2009 (UTC)

GH category page, order of families

• It would be nice if the glycoside hydrolase pages under the category link were ordered numerically; perhaps a tabulated series of links could be created in numercial order? Spencer Williams
  • This is an issue with the way the Category tags are listed in alphabetical order. One work-around could be to modify the tag in each page with a sort key. See http://meta.wikimedia.org/wiki/Help:Category#Sort_key Harry Brumer 05:21, 29 July 2009 (CEST)
  • Fixed: added sort keys in the format "GH001" to all existing pages during the first week of August 2009 (at Cellulase GRC). Harry Brumer 20:42, 6 August 2009 (UTC)

Automated lisiting of references in bibliography

The use of the pmid and isbn tags for inserting references is great. Is it possible to include doi's? This would be good for papers that are not in pubmed. If there something fancy that could be done using CrossRef?Spencer Williams 02:20, 1 September 2009 (UTC)