Related Tools & Database

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List the other available tools and databases related to glycoproteins and glycosyltransferases.
Databases and Tools
Aglgenes Database containing all available information on archaeal N-glycosylation
Animal Lectins A genomic resource of animal lectins
Bacterial Carbohydrate Structure DataBase Carbohydrate databases
BCSDB Structural, bibliographic, taxonomic and related information on bacterial carbohydrate structures (Encoding BCSDB linear code)
BRENDA Repository of Enzyme Information
CabosML Carbohydrate sequence markup Language Glycan topology description
CAZy Carbohydrate active enzymes
CFG Nomenclature Nomenclature of carbohydrates in 2D
CFG-Glycan Database Carbohydrate databases
CSDB_GT Carbohydrate Structure Glycosyltransferase Database (glycosyltransferase database on A. thaliana) Glycan fragment
dbPTM: DB of protein post-translational modification Glycans in PDBs
DOUGAL Database of glycoprotein structures Glycans in PDBs
ECODAB Escherichia coli O-antigen database
Elution Coordinate DB Database of 2-aminopyridine labelled glycans
EMBL Nucleotide Sequence Database
EMBL-CDS Nucleotide sequence database of coding sequences features
EPS database Provides access to detailed structural, taxonomic and bibliographic information on bacterial exopolysaccharide structures and properties
EUROCarbDB European Depository and Portal for carbohydrate (Encoding GlycoCT)
Genbank Nucleotide Sequence database
Genomics Resource for Animal Lectins Glycan binding proteins database contains animal lectins genomics resource includes information on the structure and function of proteins in each group
GGDB human glycogenes Glycan processing pathways and enzymes
GLYCAM Generation of 3D structures GLYCAM-web is dedicated to simplifying the prediction of three-dimensional structures of carbohydrates and macromolecular structures involving carbohydrates.
Glyco3D 3D structures of carbohydrates, glycosyltransferases and lectins
GlycoepitopeDB Database of carbohydrate recognition motifs, recognising anti-bodies and glycoproteins/glycolipids carrying the motifs
GlycoFish A database of zebrafish N-linked glycoproteins identified using SPEG method coupled with LC/MS
GlycoFly A database of Drosophila N-linked glycoproteins identified using SPEG--MS techniques
GlycoGene Database (GGDB A database of human genes associated with glycan synthesis such as glycosyltransferase, sugar nucleotide synthases etc
GlycoMapsDB Conformational maps of carbohydrates
GlyConnect Gathers sources of information for assisting in the characterization of the molecular components of protein glycosylation. GlyConnect contains curated glycan structure information extracted from the literature and has been built up from GlycoSuiteDB.
GlycoPep DB Database of N linked glycan structures derived from biologically relevant glycopeptides
GlycoPep DB MS glycan analysis tool
GLYCOSCIENCES modelling toolbox Glycan 3D modelling Collection of tools and databases for glycobiology Encoding (LINUCS)
GlycoStore A database of retention properties for glycan analysis
GlycoSuite Proteome Systems Carbohydrate databases
GlycoSuiteDB A curated database of glycoprotein glycans.
GLYDE GLYcan data exchange standard Glycan topology description
GlyTouCan International glycan structure repository that assigns globally unique accession numbers to any glycan
GPI anchor biosysnthesis Glycan processing pathways and enzymess
IUPAC Nomenclature of Carbohydrates Nomenclature of carbohydrates
IUPHAR DATABASE An annotated and expert reviewed database of Mammalian Glycoprotein hormone receptors
JCGGDB Database of Glyco genes, glycoproteins, lectin affinity, MS data, epitopes (Encoding CabosML)
KegDraw Glycan topology description
KEGG orthology glycosyltransferases Glycan processing pathways and enzymes
KEGG pathway carbohydrate metabolism It is a collection of manually drawn pathway maps representing our knowledge of the molecular interaction, reaction and relation networks for metabolism, genetic information processing, environmental information processing, cellular processes, organismal systems, human diseases, drug development.
KEGG Pathway Database Carbohydrate metabolism pathways
KEGG-Glycan KEGG Carbohydrate databases
Lectin Database A searchable database of Lectins from Algal, Animal, Bacterial, Fungal, Yeast, Plant, Virus
Lectin Frontier DataBase (LfDB) carbohydrate�protein interaction data
Lectines 3D structure of lectins Glycan binding proteins database
LiGraph Graphical representation Glycan topology description
LINUCS Linear encoding of sugars Glycan topology description
MCAW-DB A glycan profile database capturing the ambiguity of glycan recognition patterns.
National Center for Biotechnology Information Resource for Biomedical and Genomic information
NCBI Taxonomy Browser Database of Taxonomic Information
Nucleotide Database of sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data
PDB - Repository DB of all 3D bio-structures The RCSB PDB builds upon the data by creating tools and resources fro research and education in molecular biology, structural biology, computational biology, and beyond.
PDB2LINUCS Glycoproteins in PDB Glycans in PDBs
PubMed Literature Resource
RCSB PDB Database of Protein structures
SphinGOMAP pathways of sphingolipid biosynthesis It is an evolving pathway map for sphingolipid biosynthesis that includes many of the known sphingolipids and glycosphingolipids arranged according to their biosynthetic origin.
STRING Database of known and predicted protein interactions
UniCarb-DB continuation of the EUROCarbDB, repository for Glycan mass spectrometric data and structural assignment based on fragmentation data
UniProtKB (Protein knowledgebase) Resource of protein sequence and functional information
YinOYang Glyco-, phosphorylation Server produces neural network predictions for O-β-GlcNAc attachment sites in eukaryotic protein sequences.
Links to web based resources for carbohydrates
CFG- Microarray Data Glycogene chip Glycan binding protein database presents gene expression data from analyses of human and murine samples on the CFG's glycogene micoarray chip
CFG-GBP-DB glycan binding protein Glycan binding proteins database offer detailed information about individual GBPs, integrating data obtained by the CFG's scientific cores with information from public databases.
EpitopeXtractor Compare glycan structures of Glydin' network's collection
GAG-DB 3D structures of glycoaminoglycans
GBP Glycan-motif database Glycan binding protein database
Glyco@Expasy Zooming in on web-based glycoinformatics resources
GlycoEpitope DB Antibodies for glyco epitopes Glycan binding protein database
GlycoMod Possible oligosaccharide structures on proteins from masses
GlyConnect Compozitor Contextualises glycan composition sets
GlycoSiteAlign Multiple alignment of sequences around glycosylatio sites
Glydin' Network representationn of known glycan determinants
Glynsight Visualise and comapre glycan expression profiles
GlyS3 Match a glycan substrate to a database of full structures
HMO-Glycologue Simulator of Human Milk Oligosaccharide synthesis
LectinDB: Plant lectin database Glycan binding protein database
Shape Prediction of carbohydrate conformational space
SugarBind Pathogen sugar-binding database
SugarBindDB: Bacterial lectin database Glycan binding protein database
SugarSketcher Fast, intuitive, SNFG-compliant glycan structure drawing
Swiss Mass Abacus Intuitive calculator of peptide and glycopeptide masses
UniLectin Structural and functional classification of lectins
dbCAN A web server and DataBase for automated Carbohydrate-active enzyme Annotation
dbCAN2 A meta server for automated carbohydrate-active enzyme annotation
Glycan A database of PDB-based glycan 3D structures
Glycan Library A list of approximately 830 lipid-linked sequence-defined glycan probes derived from diverse natural sources or chemically synthesised
GlycoDigest A tool that simulates exoglycosidase digestion
GlycoDomain Viewer For Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology
GlycoPattern A web resource for glycan array mining
GlyMAP An online resource mapping out the variational landscape of glyco-active enzymes
RINGS Resource for Informatics of Glycomes at Soka
MS Tools
GlycanMass Calculation of the mass of an oligosaccharide structure from its composition
GlycReSoft Tool for automated recognition of glycans from LC-MS data
GPQuest Tool for identification of intact N- and O-linked glycopeptides in HCD proteomics mass spectrometry data
MAGIC-web Web server aiming to provide mass spectrometry-based automated glycoprotein identification service
MassyTools A High-Throughput Targeted Data Processing Tool for Relative Quantitation and Quality Control Developed for Glycomic and Glycoproteomic MALDI-MS.
NMR Tools
CASPER 1H, 13C-NMR estimation GLycaStructure analysis of Glycans by NMR chemical shift prediction
CCPN Website of the Collaborative Computing Project for NMR
GlyNest Estimation of NMR chemical shifts
NMR-Search 1H, 13C-NMR search Glycan NMR tool is an external tool that enables a peak search by both 1H and 13C shifts.
SugarBase 1H, 13C-NMR search Glycan NMR tools
Glycan structure/conformation Tool
3D SNFG Generates 3D shapes of glycans that match the SNFG format (Symbol Nomenclature for Glycans)
CSBD/SNFG Structure editor An Online Glycan Builder with 2D and 3D Structure Visualization
Links to web based Resources for Glycoconjugates
Glycoproteomics MS Tools
Glycanfragment Masses from glycan fragments Glycan MS tools, an annotated data collection linking glycomics and proteomics data
Glycoforest Partial de novo glycan sequencing method based on MS/MS data
GlycoMod Glycan composition from molpeak Glycan MS tools, predict possible oligosaccharide structures that occur on proteins from their experimentally determined masses. The program can be used for free or derivatized oligosaccharides and for glycopeptides.
GlycoSearchMS MS-spectra comaprison Glycan MS tool, to search for specific carbohydrate chains in the PDB, which is not possible at the PDB interfaces so far.
GlycosidIQ Glycofragment mass fingerprinting Glycan MS tool
GlycoWorkbenh - MS analysis tool suite Glycan MS tool
GRITS Toolbox A glycomics MS data processing tool
MzJava Open source Java class library to process MS fragmentation
PepSweetener Human intact N-glycopeptide mass matching tool
pGlyco Identification of intact glycopeptides by integrating HCD-MS/MS, CID-MS/MS and MS3 information.
SimGlycan Glycan and glycopeptide MS/MS data analysis tool
Tools for prediction and analysis of glycosylation sites/ residues
Big-PI GPI anchor prediction server
CKSAAP_OGlySite O-glycosylation prediction server
DAGR Database of Anti-Glycan Reagents -use to search and identify antibodies and reagent lectins to various carbohydrate
EnsembleGly N,O and C-glycosylatin prediction server
FindMod Peptides with experimentally measured masses are characterized for possible modifications
FragAnchor GPI anchor prediction server
GECS N-Glycan Prediction Server is collection of methods for prediction of possible N glycan structures based on the repertoire of glycosyltransferases for N-glycan biosynthesis.
GlycoEP In silico Platform for Prediction of N-, O- and C-glycosites in Eukaryotic Protein Sequences
GlycoMinestruct A new bioinformatics tool for highly accurate mapping of the human N-linked and O-linked glycoproteomes by incorporating structural features
GlycoPP GlycoPP: a webserver for prediction of N- and O-glycosites in prokaryotic protein sequences
GPI-SOM Prediction of GPI-anchors
GPP Prediction of O- and N-glycosylation
ISOGlyP Isoform specific O-glycosylation prediction
NetCGlyc C-mannosylation prediction server
NetNGlyc N-glycosylatin prediction server
NetOGlyc O-glycosylation prediction server
NGlycPred Server N-linked Glycosylation Prediction Server Incorporating Structural Information and Patterns
Oglyc O-glycosylation prediction server
PredGPI GPI anchor prediction server
PTM prediction-User Interface List of available PTM prediction servers
Structural Assessment of Glycosylation (SAGS) Prediction of glycosylation sites
YinOYang O-glycosylation prediction server
Tools for Glycoprotein Structure/ Conformation
doGlycans Tools for Preparing Carbohydrate Structures for Atomistic Simulations of Glycoproteins, Glycolipids, and Carbohydrate Polymers for GROMACS
Dynamic Molecules Online molecular dynamics (MD) simulations
GLYCAM N-glycans modeled onto it using the online portal
Glydict Prediction of N-glycan 3D structures
GlyProt Modeling 3D structure of glycoproteins with attached N-glycans
GlySeq Statistical analysis of residues neighbouring N-glycan sequons in protein sequence
GlyVicinity Statistical analysis of residues surrounding carbohydrate chains in protein 3D structure
GROMACS Molecular dynamics simulations
GS-align For glycan structure alignment and similarity measurement
SWEET-II Building 3D carbohydrate models
SweetUnityMol Software to display 3-D structures of carbohydrates, polysaccharides and glycoconjugates