O-Glycologue
Getting started
Enter a glycan | Choose enzymes | React or Predict |
Choose a starting substrate in GlycoForm* | Optionally, knock out one or more enzymes in silico | Present this glycan as a substrate to the enzymes of O-linked glycosylation Predict the enzymes required to produce this glycan |
*To select from a library of experimentally derived O-glycans, click here
Features
- Glycans can be entered via a linear IUPAC condensed name, or in the simulator's native format
- Submitting a structure to the enzymes of O-linked glycosylation will generate networks of possible reactions
- Predicted glycan structures are displayed in a grid
- Glycans can be displayed in SNFG or UOXF notation, and in Linear Code, IUPAC or GlycoCT condensed formats
- Predict the enzymes required for the biosynthesis of a given glycan
- Knock out enzymes singly or in combination and observe the effects on the distributions of clinically important epitopes, such as Lewis-x, -y, -a or -b
- Set a baseline knockout to compare against further knockouts
- Graph the reaction networks (up to 5000 O-glycans)
- Download reaction networks as SBML (Systems Biology Markup Language)
- Networks, and individual glycans, can be downloaded as SVG or PDF vector images
Source
Source code of the enzyme simulator implemented in Python 3 can be downloaded here
Publications
McDonald., A.G, Tipton, K.F. and Davey, G.P. (2016) A knowledge-based system for display and prediction of O-glycosylation network behaviour in response to enzyme knockouts. PLoS Comp. Biol. 12(4), e1004844. [doi: 10.1371/journal.pcbi.1004844]McDonald, A.G. and Davey, G.P. (2021) Simulating the enzymes of ganglioside biosynthesis with Glycologue. Beilstein J. Org. Chem. 17, 739-748. [doi: 10.3762/bjoc.17.64]
McDonald A.G., Mariethoz J., Davey G.P. and Lisacek, F. (2022) In silico analysis of the human milk oligosaccharide glycome reveals key enzymes of their biosynthesis. Sci. Rep. Jun 27;12(1):10846. doi: 10.1038/s41598-022-14260-4]
