Glycologue

Description: Glycologue is a simulator of the enzymes of human-milk oligosaccharide (HMO) biosynthesis, developed and maintained by Andrew McDonald (School of Biochemistry & Immunology, Trinity College Dublin). This work is supported through the Swiss Institute of Bioformatics grant number SNSF: 31003A_179249.

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 human-milk oligosaccharide (HMO) biosynthesis    Predict the enzymes required to produce this glycan

*To select from a library of experimentally derived Human milk oligosaccharides, 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 human-milk oligosaccharide (HMO) biosynthesis 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 HMOs)
• 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]