Table 1.
Summary of representative glycoinformatic databases.
| Name | Description | Retrievable by | URL |
|---|---|---|---|
| Glycan structure databases | |||
| CFG glycan structure database [14] | Database providing structural and chemical information on thousands of glycans, including both synthetic glycans and glycans for mammalian species. | Searched by glycan names, composition, molecular weight, motifs, cell lines or tissue samples. | http://www.functionalglycomics.org/glycomics/molecule/jsp/carbohydrate/carbMoleculeHome.jsp |
| JCGGDB Glycan Mass spectral DataBase [16] | Database containing multi-stage tandem mass spectral of structurally defined N-and O-linked glycans, and glycolipid glycans. | Searched by glycan composition or m/z value of precursor ion. | https://jcggdb.jp/rcmg/glycodb/Ms_ResultSearch |
| UniCarbKB [25,26,27] | A curated database of information on glycan structures of glycoproteins, with descriptions of its biological source, supporting reference and experimental methods. | Searched by monosaccharide composition, attached protein, taxonomy or tissue by using an auto completion feature. | http://unicarbkb.org/ |
| KEGG glycan [13] | Database providing information on experimentally determined glycan structures and their metabolic pathways. | Searched by the G number for each glycan structure. | http://www.genome.jp/kegg/glycan/ |
| GLYCOSCIENCE.de [12,33] | An integrated portal containing databases and tools mainly glycan 3D structure analysis. | Searched by monosaccharide composition, molecular formula, structure classification and motifs, as well as NMR atoms or peaks. | http://www.glycosciences.de/ |
| Glycosciences.DB [35] | The main glycan structure database of GLYCOSCIENCE.de, providing published data on glycan structures, their taxonomy, MS and NMR-experimental data, 3D structure models as well as references to PDB entries. | Searched by glycan (sub-)structure, monosaccharide composition, molecular formula, structure classification and motifs, as well as NMR, MS, PDB query, or bibliography queries. | http://www.glycosciences.de/database/ |
| UniCarb-DB [36] | Database providing LC-MS/MS data of glycan structures. | Searched by taxonomy, tissue, reference, mass, composition or precursor mass. | https://unicarb-db.expasy.org/ |
| GlyTouCan [37] | A international glycan sequence repository with a globally unique accession number assigned to each structure. | Searched by text input, motif, or drawing glycan structures in GlycanBuilder. Registered users can additionally register new glycan structures to obtain unique IDs for each structure. | https://glytoucan.org/ |
| GlycoStore [41] | A curated database of information on glycan retention properties with chromatographic, electrophoretic and mass-spectrometry composition data. | Searched by experimental values (GU, AU or time), monosaccharide composition or metadata labels (taxonomy, sample name and the Oxford linear notation). | https://www.glycostore.org |
| CSDB [42] | Database on the structures of glycans and glycoconjugates in prokaryotes, plants and fungi. | Searched by CSDB ID, glycan substructure, composition, taxonomy, bibliography, NMR signals, conformation ID or GT name. | http://csdb.glycoscience.ru/database/ |
| Glycoprotein databases | |||
| GlycoProtDB [56] | Database providing information on N-glycoproteins and their glycosylated site(s) identified from C. elegans, mouse tissues and human. | Searched by gene ID, gene name, and its description (protein name). | https://acgg.asia/db/gpdb2/ |
| UniPep [59] | Database providing information on N-glycopeptides identified from human plasma and tissues including bladder, breast, liver, lymphocytes, cerebrospinal fluid, and prostate. | Searched by gene name, gene symbol, Swiss Prot ID, IPI ID, protein sequence or peptide mass. | http://www.unipep.org/ |
| N-GlycositeAtlas [22] | Database providing information on N-glycopeptides identified from over 100 publications and unpublished datasets | Searched by gene/protein name, accession number, glycosylation site location, glycosite containing peptide, tissue/liquid/cell line, or publication | http://nglycositeatlas.biomarkercenter.org |
| GlycoDomain Viewer [95] | Database of O-GalNAc proteinsidentified by SimpleCell technology from human and animal cell lines, associated with the verified and predicted glycosylated sites of N-glycan, O-GalNAc, O-Mannose and O-Xylose mapping on the protein sequence | Searched by the NCBI gene name or the Uniprot ID | https://glycodomain.glycomics.ku.dk/ |
| Glycogene databases | |||
| CAZy [62] | The largest database for display and analysis of genomic, structural and biochemical information on glyco-enzymes | Searched by enzyme family, protein name, organism name, GeneBank or UniProt accession, or EC number. | http://www.cazy.org/ |
| CAZypedia [63] | A comprehensive encyclopedic of detailed structural, and biochemical information on glyco-enzymes, and relevant reference. | Searched by enzyme name or enzyme ID | http://www.cazypedia.org |
| GlycoGene DataBase [15] | Database providing information of glycogenes on gene sequences, substrate specificities, homologous genes, EC numbers, tissue distribution, KO mouse as well as external links to various databases. | Searched by gene symbols or designations or selected from the list of glycogenes | https://acgg.asia/ggdb2/ |
| CFG glycosyltransferases database | Database providing information of glycosyltransferase on enzyme name, EC number, organism, relevant CFG data, and other data from public databases (PubMed, KEGG, CAZy, SwissProt, and others). | Providing a graphical interface of different glycans. By clicking a monosaccharide, users are directed to the information of the glycosyltransferase which forms this structure. | http://www.functionalglycomics.org/glycomics/molecule/jsp/glycoEnzyme/geMolecule.jsp |
| CSDB_GT [96] | A curated database of glycosyltransferases in Arabidopsis thaliana, Escherichia coli and Saccharomyces cerevisiae. | Searched by CSDB ID, glycan structure, composition, taxonomy, bibliography, NMR signals, conformation, or GT activity. | http://csdb.glycoscience.ru/gt.html |
| Glycan-protein interaction database | |||
| Lectin Frontier Database [67] | Database providing quantitative interaction data between various glycan and lectins, as well as basic information such as kingdom, monosaccharide specificity on lectins | Searched by keyword or choose categories among Lectin family, Monosaccharide Specificity, or 3D-fold. | http://acgg.asia/lfdb2/ |
| UniLectin [68] | A interactive database for the classification and curation of lectins (with UniLectin3D module), and the prediction of β-propeller lectins (with PropLec module). | Searched by keywords, kingdom order, historical classification, monosaccharide, associate IUPAC sequence, fold of the binding site, or multiple criteria | https://www.unilectin.eu/ |
| PACDB [69] | Database providing information on the interaction of microbial glycan-binding proteins and glycans with host glycan ligands | Selected from the list of disease, pathogen names, monosaccharides, or glycoepitopes | https://acgg.asia/db/diseases/pacdb |
| SugarBindDB [70] | A curated database providing information on known glycan structure interacted with pathogenic organisms (bacteria, toxins and viruses) in various disease | Searched by pathogenic agents, ligands, recognizing lectins, affected area, references, diseases or multi-criteria. | https://sugarbind.expasy.org/ |
| GLAD [71] | A web-based tool to visualize, analyze, present, and mine glycan array data. | Input data as tab-delimited text files in the correct format | https://glycotoolkit.com/Tools/GLAD/ |
| MCAW-DB [72] | Database providing information on binding affinity of glycan binding proteins to glycan substructures by multiple alignment analysis of glycan array data | Searched by filtering taxa, protein family, investigator and array version. | https://mcawdb.glycoinfo.org/ |
| GlyMDB [73] | Database enabling users to upload their own microarray data, query binder/non-binder classification, discover glycan-binding motif, compare glycan array sample, and cross-link microarray samples to PDB structures | Searched by protein name, protein sequence or PDB ID, or upload microarray spreadsheet file. | http://www.glycanstructure.org/ |
| MatrixDB [74] | A curated database providing information on interactions between extracellular matrix proteins, proteoglycans and polysaccharides. | Searched by a biomolecule, keyword, author, publication or IMEx identifier. | http://matrixdb.univ-lyon1.fr/ |
| Latest integrated glycoscience portal | |||
| Glycomics@ExPASy [19] | The glycomics tab of ExPASy, centralizing web-based glycoinformatics databases and tools resources developed by SIB (such as GlyConnect, SugarBind and UniCarb-DB databases) and other external resources to (such as CAZy, CSDB, GlyTouCan and UniCarbKB) to bridge the glycobiology and protein-oriented bioinformatics resources | Click on the link of interest | https://www.expasy.org/glycomics |
| GlyConnect [86] | The central platform of the Glycomics@ExPASy, providing interactive diagrams that help the user understand relations between glycans, proteins, tissues, diseases, and taxonomy | Either browsed or searched by protein name, ID, or monosaccharide composition, linkage type | https://glyconnect.expasy.org/ |
| Glygen [18] | A web portal data integration, harmonization and dissemination web portal for integrate data and knowledge from diverse disciplines relevant to glycobiology, carbohydrate and glycoconjugate-related data retrieved from multiple international data sources including UniProtKB, GlyTouCan, UniCarbKB and other key resources. | Searched by protein accession, sequences, glycan structure or monosaccharide composition. | https://glygen.org/ |
| GlyCosmos [20] | An integrated web resource including the database of JCGGDB and providing information on glycan-related genes, proteins, lipids, glycomes, pathways and diseases to integrate the glycosciences with the life sciences | Searched by protein name, protein accession, species, or various glycan search tools, such as by mass, composition, graphical glycan structure or monosaccharide composition. | https://glycosmos.org |