GlyTouCan 1.0 – The international glycan structure repository

Abstract

Glycans are known as the third major class of biopolymers, next to DNA and proteins. They cover the surfaces of many cells, serving as the ‘face’ of cells, whereby other biomolecules and viruses interact. The structure of glycans, however, differs greatly from DNA and proteins in that they are branched, as opposed to linear sequences of amino acids or nucleotides. Therefore, the storage of glycan information in databases, let alone their curation, has been a difficult problem. This has caused many duplicated efforts when integration is attempted between different databases, making an international repository for glycan structures, where unique accession numbers are assigned to every identified glycan structure, necessary. As such, an international team of developers and glycobiologists have collaborated to develop this repository, called GlyTouCan and is available at http://glytoucan.org/, to provide a centralized resource for depositing glycan structures, compositions and topologies, and to retrieve accession numbers for each of these registered entries. This will thus enable researchers to reference glycan structures simply by accession number, as opposed to by chemical structure, which has been a burden to integrate glycomics databases in the past.

How and why plants and human N-glycans are different: Insight from molecular dynamics into the “glycoblocks” architecture of complex carbohydrates

“…These complexities are very difficult to resolve, requiring high levels of expertise and multi-layered orthogonal approaches [8][9][10]7]. Within this framework, the contribution of glycoinformatics tools and databases represents an essential resource to advance glycomics [11][12][13][14][15], while molecular simulations fit in very well as complementary and orthogonal techniques to support and advance structural glycobiology research. Indeed, current high performance computing (HPC) technology allows us to study realistic model systems [16,17] and to reach experimental timescales [18], so that computing can now contribute as one of the leading research methods in structural glycobiology.…”

Correcting for sparsity and non-independence in glycomic data through a systems biology framework

“…First, glycoprofiles are parsed into glycans with abundance. In each glycoprofile, the glycans are manually drawn and exported with GlycoCT format using the GlyTouCan Graphic Input tool 13 . GlycoCT formatted glycans are loaded into Python (version 3+) and initialized as glypy.glycan objects using the glypy (version 0.12.1).…”

“…First, glycoprofiles are parsed into glycans with abundance. In each glycoprofile, the glycans are manually drawn and exported with GlycoCT format using the Glytoucan Graphic Input tool 13 . The structure of glycan in GlycoCT format will be further loaded into python using “glypy” (a glycan analysis and glycoinformatics library for Python) for programmatic manipulation.…”

“…Advances in mass spectrometry now enable the rapid generation of large volumes of glycoprofiles with detailed glycan composition 7–10 , exposing the complex and heterogeneous glycosylation patterns on lipids and proteins 11,12 . Large glycoprofile datasets and supporting databases are also emerging, including GlyTouCan 13 , UnicarbDB 14 , Glygen and UniCarbKB 15 .…”

Mass Spectrometry-Based N-Glycomics of Colorectal Cancer

“…In addition to these (semi) automated tools for analysis of glycan data from LC-MS/MS data, efforts have been made towards integrating a number of glycomics-centric databases into a common platform called UnicarbKB [ 149 ] and UnicarbDB [ 150 ], which act as centralized data repositories for glycan data and work on the interface with the already available glycomics (GlycomeDB, EUROcarbDB) and proteomics (Uniprot) databases [ 151 , 152 ]. Other glyco-related databases include Glycosciences.de, Kyoto Encyclopaedia of Gene and Genomes Glycans (KEGG Glycans), and the consortium for functional glycomics (CFG) and the more recently developed GIyTouCan ( ) [ 153 ].…”