The glyenzy package helps simulate the biosynthetic process of glycosylation in silico. Key features include: identifying the specific glycosyltransferase responsible for each glycosidic bond; reconstructing the biosynthetic pathway of a given glycan; exploring possible transformations between two glycan structures via glycosyltransferases and glycosidases; and predicting the glycans that can be synthesized from a given substrate structure and a set of enzymes.
Installation
You can install the latest release of glyenzy from GitHub with:
# install.packages("remotes")
remotes::install_github("glycoverse/glyenzy@*release")Or install the development version:
remotes::install_github("glycoverse/glyenzy")Role in glycoverse
As one of the most downstream components of the glycoverse ecosystem, this package builds on glyrepr, glyparse, and glymotif, with planned integration with glydraw. It is intended for direct use by omics researchers, providing practical, analysis-ready insights into glycan biosynthesis.
Example
Say we have a glycan…
glycan <- "Gal(b1-4)GlcNAc(b1-6)[Gal(b1-3)]GalNAc(a1-"And you want to know what enzymes participates in the biosynthesis of this glycan…
get_involved_enzymes(glycan)
#> [1] "B4GALT1" "B4GALT2" "B4GALT3" "B4GALT4" "B4GALT5" "C1GALT1" "GCNT1"
#> [8] "GCNT3" "GCNT4"Here you go!
What if you’re curious of what new glycans can by generated by applying ST3GAL2?
apply_enzyme(glycan, "ST3GAL2")
#> <glycan_structure[1]>
#> [1] Neu5Ac(a2-3)Gal(b1-3)[Gal(b1-4)GlcNAc(b1-6)]GalNAc(a1-
#> # Unique structures: 1