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GLYCAM-Web / website

A bare-bones repo to contain public website stuff and issues related to the GLYCAM Web Django apps.
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Providing rationale to the user for "likely structures" vs "possible structures" #183

Closed holmess2013 closed 1 week ago

holmess2013 commented 4 months ago

Is your feature request related to a problem? Please describe.

When a user builds a carbohydrate that features a 1-->6 linkage, for example, you now have options for different glycosidic linkage torsion angles (gg, gt, tg, etc.). Further, there are two boxes that will list the number of "possible structures" and then the number of "likely structures", but there isn't any information listed for why some are likely and others are not. I believe that they are chosen based off the results from certain journal articles that should be provided to the user.

Describe the solution you'd like

To remedy this, we should provide journal articles that will provide that answer depending on the linkages that the user included in their carbohydrate. If they only have a 1->6 linkage, then we should direct them to a page with links to the journal articles that will discuss glycosidic torsion preferences for that linkage. If they included a Neu5Aca2-3X linkage, then send them to a different page with links for that. If both, then a page that has links for both.

Describe alternatives you've considered

Another way to do it to cut down on the number of pages needed is direct the user to a single page with all the links to journal articles, but then highlight the links that correspond to the linkage that the user included in their carbohydrate.

gitoliver commented 3 months ago

I sent Rob a draft of the page to edit. I'll post the text here when I get it.

gitoliver commented 3 months ago

Background Glycosidic linkages can populate more than one conformation in solution, depending on the constituent monosaccharides and linkage type. The conformation of each glycosidic bond is measured using dihedral angles labelled as phi, psi or omega for the first, second and (if present) third bond of the linkage.

"Possible" vs "Likely" Rotamers The population of glycosidic linkage rotamers depends on the type of monosaccharides involved as well as the linkage positions. Additionally, steric interactions and the exo-anomeric effect further restrict the population of the rotamers, resulting in a set of most likelys shapes. However, you may also generate and download all possible rotamers if desired.

Further reading: The discussion around Figures 4-6 in Nivedha et al "Importance of Ligand Conformational Energies in Carbohydrate Docking: Sorting the Wheat from the Chaff" JCC 2014.

danwentworthart commented 3 months ago

I have pushed this. It has not been deployed yet.