diff --git a/webserver/public/Cremer-Pople.png b/webserver/public/Cremer-Pople.png index 2715bd90..fb913b35 100644 Binary files a/webserver/public/Cremer-Pople.png and b/webserver/public/Cremer-Pople.png differ diff --git a/webserver/public/glycomics.png b/webserver/public/glycomics.png new file mode 100644 index 00000000..25636443 Binary files /dev/null and b/webserver/public/glycomics.png differ diff --git a/webserver/public/refmac_figure.png b/webserver/public/refmac_figure.png new file mode 100644 index 00000000..e04c6b89 Binary files /dev/null and b/webserver/public/refmac_figure.png differ diff --git a/webserver/public/torsion_figure.png b/webserver/public/torsion_figure.png new file mode 100644 index 00000000..4341d248 Binary files /dev/null and b/webserver/public/torsion_figure.png differ diff --git a/webserver/src/components/Information/Information.tsx b/webserver/src/components/Information/Information.tsx index be4839b0..e1c0bef5 100644 --- a/webserver/src/components/Information/Information.tsx +++ b/webserver/src/components/Information/Information.tsx @@ -1,38 +1,58 @@ -export function Information() { +import {TORSIONS_CITATION, GLYCOMICS_CITATION} from "../../data/Constants" + +export function Information({}) { return
- How does it work? - Privateer mainly uses three properties to assess the validity of a glycan chain. + How does it work? + + Carbohydrates, including O- and N-glycans attached to protein and lipid structures, are increasingly important in cellular biology. Crystallographic refinement of sugars is, however, very poorly performed, with thousands of incorrect structures polluting the Protein Data Bank. Privateer is a software that aims to detect and prevent conformational, regiochemical and stereochemical anomalies in cyclic carbohydrate structures. Multiple features can be used to assess the validity of a glycan chain.
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- Stereochemical Validation + Stereochemical Validation - Cyclic carbohydrates usually have clear conformational preferences in terms of energy. Enzymes can force sugars into higher-energy conformations in order to achieve catalysis, and these conformations should indeed be kept in mind when modelling a sugar in the -1 site of an enzyme. However, most of the time ( i.e. in the rest of the cases) sugars stay in their original lowest-energy conformation, which for pyranoses is either a 4C1 or a 1C4 chair. - Privateer checks each glycan for the correct stereochemistry and highlights when and where there are issues. + Cyclic carbohydrates usually have clear conformational preferences in terms of energy. Whilst enzymes can force sugars into higher-energy conformations in order to achieve catalysis, sugars tend to stay in their original lowest-energy conformation, which for pyranoses is either a 4C1 or a 1C4 chair. Privateer checks each glycan for the correct stereochemistry and highlights any outliers.
- Real Space Correlation Coefficient Validation - The real space correlation coefficient metric in quantitative terms describes how well a modelled residue fits its associated experimental density, by calculating the difference between observed(experimental) structural factors and calculated structural factors associated with the fitted model. For monosaccharides that are modelled as components of glycans, RSCC values of above 0.80 are considered to signify a good model fit to its associated experimental density. + Real Space Correlation Coefficient Validation + The real space correlation coefficient metric quantitatively describes how well a modelled residue fits its associated experimental density. It is defined by calculating the difference between observed (experimental) structural factors and calculated structural factors associated with the fitted model. For monosaccharides that are modelled as components of glycans, RSCC values of above 0.80 are considered to signify a good model fit to its associated experimental density. A real space correlation coefficient against omit mFo-DFc electron density is reported as a quality of fit indicator.
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- Anomer Validation - Occasionally, the glycans modelled in a structure can exhibit anomeric configurations which have not been seen before, and are most likely the result of slightly incorrect glycan positioning. Privateer can highlight this to allow a user to correct the mistakes. + Glycomics-Powered Validation + + + + + When modelling glycans, it is possible to produce incorrect glycan compositions that do nor conform with general glycan biosynthesis knowledge. In Privateer, users can check their glycan structure and composition against glycomics databases. This allows the identification of inconsistent linkages, and following this, alternative compositions will be suggested to provide a more accurate, complete structure. +
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+ Torsion Angles + + + + + + + Torsion angle analysis allows the validation of the overall conformation of N-glycans. Using a compiled set of glycosidic linkage torsional preferences harvested from a curated set of glycoprotein models, a Z score for each proposed glycan linkage is calculated and displayed within the Symbol Nomenclature For Glycan (SNFG) image.
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diff --git a/webserver/src/data/Constants.tsx b/webserver/src/data/Constants.tsx index 23b6da76..921f21de 100644 --- a/webserver/src/data/Constants.tsx +++ b/webserver/src/data/Constants.tsx @@ -1,5 +1,7 @@ export const GITHUB_REPO = "https://github.com/glycojones/privateer" export const GENERAL_CITATION = "" +export const TORSIONS_CITATION = "http://dx.doi.org/10.1107/S2059798323003510" +export const GLYCOMICS_CITATION = "https://doi.org/10.3762/bjoc.16.204" export const COLUMNS = [ {