Related Tools & Database


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List the other available tools and databases related to glycoproteins and glycosyltransferases.
Databases and Tools Cross Referred in ProGlycProt
DatabaseDescription
National Center for Biotechnology Information Resource for Biomedical and Genomic information
PubMed Literature Resource
NCBI Taxonomy Browser Database of Taxonomic Information
Genbank Nucleotide Sequence database
EMBL Nucleotide Sequence Database
Nucleotide Database of sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data
EMBL-CDS Nucleotide sequence database of coding sequences features
UniProtKB (Protein knowledgebase) Resource of protein sequence and functional information
RCSB PDB Database of Protein structures
BRENDA Repository of Enzyme Information
STRING Database?of?known?and?predicted?protein?interactions
BCSDB Structural, bibliographic, taxonomic and related information on bacterial carbohydrate structures (Encoding BCSDB linear code)
CAZy Carbohydrate active enzymes
O-GLYCBASE A revised database of O- and C-glycosylated proteins
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.
GlyTouCan International glycan structure repository that assigns globally unique accession numbers to any glycan
Links to web based resources for carbohydrates
DatabaseDescription
JCGGDB Database of Glyco genes, glycoproteins, lectin affinity, MS data, epitopes (Encoding CabosML)
CFG Websites of the Consortium for Functional Glycomics. Databases of Glycans, lectins, glycosyltransferases (Encoding Glycominds Linear Code)
Glycoconjugate Data Bank Resource for Carbohydrate related literature, networks and structures
EUROCarbDB European Depository and Portal for carbohydrate (Encoding GlycoCT)
GLYCOSCIENCES.de Collection of tools and databases for glycobiology Encoding (LINUCS)
RINGS Resource for Informatics of Glycomes at Soka
CCSDB/CarbBank Complex Carbohydrate Structure Database, first &largest carbohydrate database with 50?000 records of around 15?000 different carbohydrate structures (encoding IUPAC extended)
KEGG Glycan collection of experimentally determined glycan structures (Encoding KCF)
UniCarb-DB continuation of the?EUROCarbDB, repository for Glycan mass spectrometric data and structural assignment based on fragmentation data
Sugabase Carbohydrate-NMR database that combines CarbBank data with chemical shift values
GlycoMapsDB Conformational maps of carbohydrates
DisaccharideDB Conformational maps of disaccharides
KEGG Pathway Database Carbohydrate metabolism pathways
BPGD Bacterial Polysaccharide Gene Database
KEGG Orthology Database KEGG Orthology (KO) groups for glycosyltransferases
GlycoGene Database (GGDB A database of human genes associated with glycan synthesis such as glycosyltransferase, sugar nucleotide synthases etc
CFG glycosyltransferase database A database of GTs
CERMAV glycosyltransferase database 3D structure database of glycosyltransferases
GlycoepitopeDB Database of carbohydrate recognition motifs, recognising anti-bodies and glycoproteins/glycolipids carrying the motifs
GPI Anchor Biosynthesis Report Database of enzymes for biosynthesis of GPI anchors
GlycoBase Database of 2-aminobenzamide labelled N glycan structures and exoglycosidase digestion pathways
Elution Coordinate DB Database of 2-aminopyridine labelled glycans
GlycomeDB Meta-database to search various databases via one interface
MonoSaccharideDB Reference database for monosaccharide notation
UnicarbKB UniCarbKB: building a knowledge platform for glycoproteomics
ProGlycProt ProGlycProt: a repository of experimentally characterized prokaryotic glycoproteins
UniPep UniPep--a database for human N-linked glycosites: a resource for biomarker discovery
dbOGAP dbOGAP - an integrated bioinformatics resource for protein O-GlcNAcylation
GlyAffinity Repository of curated protein?carbohydrate interaction data from various sources and techniques
CERMAV glycosyltransferase database 3D structure database of glycosyltransferases
Rice GT Database Phylogenomic Database and Identification of Rice-Diverged Glycosyltransferases
Brassica?Database Glycosyltransferase Gene Families genes in B. rapa
Aglgenes Database containing all available information on archaeal N-glycosylation
ECODAB Escherichia coli?O-antigen database
CSDB_GT Carbohydrate Structure Glycosyltransferase Database (glycosyltransferase database on A. thaliana) Glycan fragment
BOLD A biological O-linked glycan database.
Glycan A database of PDB-based glycan 3D structures
GlycoDigest A tool that simulates exoglycosidase digestion
GlycomeAtlas A tool for analyzing glycan profiling data
GlycoPattern A web resource for glycan array mining
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
GlyMAP An online resource mapping out the variational landscape of glyco-active enzymes
GlycoStore A database of retention properties for glycan analysis
MCAW-DB A glycan profile database capturing the ambiguity of glycan recognition patterns.
GLYDE-II The GLYcan data exchange format
REStLESS Automated Translation of Glycan Sequences from Residue-Based Notation to SMILES and Atomic Coordinates.
dbCAN A web server and DataBase for automated Carbohydrate-active enzyme Annotation
GlycoCD GlycoCD data bank is a manually curated, comprehensive repository of CDs which defined as distinct oligosaccharide sequences as part of either glycoproteins and/or glycosphingolipids and b) defined as proteins which have carbohydrate recognition sites (CRDs) or as carbohydrate binding lectins.
GlycO Focuses on the glycoproteomics domain to model the structure and functions of glycans and glycoconjugates, the enzymes involved in their biosynthesis and modification, and the metabolic pathways in which they participate
EK3D A repository of 72 E. coli K antigens that provides information about sugar compositions, their anomeric and enantiomeric forms and linkages between the sugar monomers.
GMDB?/ Glycan Mass Spectral DataBase Provides a multistage tandem mass spectral (MS) database using a variety of structurally defined glycans. GMDB offers a resource for glycomics research that?
SACCHARIS An automated pipeline to streamline discovery of carbohydrate active enzyme activities within polyspecific families and de novo sequence datasets
MS Tools
DatabaseDescription
GlycoWorkbench Tool for drawing of glycan structures based on glycan composition determined from their mass spectrometry data
Glyco-Peakfinder Determination of glycan composition from their mass signal, Tool for annotation of Glycan MS spectra
GlycoPep DB MS glycan analysis tool
GlycoMiner Composition analysis of N glycan chain linked to a protein
Glycofragment Calculate and display the main fragments (Band C-, Z- and Y-, A- and X-ions) of oligosaccharides that should occur in MS spectra
GlycanMass Calculation of the mass of an oligosaccharide structure from its composition
GlycoSearchMS Search GLYCOSCIENCES.de database for structures matching a given set of MS mass peaks
GlycoPeakfinder Tool for fast annotation of glycan MS spectra, results can be used for advanced database search in GLYCOSCIENCES.de
GlycosidIQ Glycofragment mass fingerprinting
Integrated GlycoProteome Analyzer For Automated Identification and Quantitation of Site-Specific N-Glycosylation
GlycoDomain Viewer For Precision mapping of the human O-GalNAc glycoproteome through SimpleCell technology
GlycReSoft Tool for automated recognition of glycans from LC-MS data
MassyTools A High-Throughput Targeted Data Processing Tool for Relative Quantitation and Quality Control Developed for Glycomic and Glycoproteomic MALDI-MS.
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
Glycopeptide Decoy Generator (GDG) Software application that generates glycopeptide decoys de novo
GlycanAnalysis Plug-in A database search tool for N-glycan structures using mass spectrometry.
gFinder Analyzes mixtures of native N glycopeptides that have been profiled by tandem mass spectrometry
GlycoMaster DB Automated Identification of N-Linked Glycopeptides by Tandem Mass Spectrometry
NMR Tools
DatabaseDescription
CASPER Simulation of NMR spectra and carbohydrate sequence determination from NMR chemical shift values
GlyNest Estimation of NMR chemical shifts
ProSpectND Integrated NMR data processing and inspection tool
CCPN Website of the Collaborative Computing Project for NMR
GODESS NMR spectrum simulation service for carbohydrate-containing molecules (including polymers and glycoconjugates)
CCPN Tools? Annotation of NMR spectra
GRASS A novel method for semi-automated elucidation of carbohydrate and derivative structures which uses unassigned 13C NMR spectra and information obtained from chromatography, optical, chemical and other methods.
HPLC Tools
DatabaseDescription
AutoGU Tool to assist the interpretation of HPLC data
GALAXY Visualization of HPLC 2-D maps
GlycoExtractor Automatic extraction of experimental HPLC data for multiple samples in various downstream analysis compatible formats
GlycoProfile assigner Automatically assign structures to HPLC/UPLC glycan analytical data
Glycan structure/conformation Tool
DatabaseDescription
Sweet-II Generation of 3D carbohydrate structure models
Glycan Builder Visual editor of glycan structure
DrawGlycan-SNFG Render glycans and glycopeptides with fragmentation info. using the Symbolic Nomenclature for Glycans [SNFG]
GlyQ-IQ Glycomics quintavariate-informed quantification with high-performance computing and GlycoGrid 4D visualization.
3D SNFG Generates 3D shapes of glycans that match the SNFG format (Symbol Nomenclature for Glycans)
Tools to predict carbohydrate 3D structures
DatabaseDescription
CARP Carbohydrate Ramachandran Plot
DrawRINGS Tool for 2D glycan structure Drawings
GlycoMaps DB Conformational maps
Disaccharides Conformational maps
Qrator A tool for web based curation of glycan structures
Gly-Spec A webtool for predicting glycan specificity by integrating glycan array screening data and 3D structure
Glycan fragment database A database of PDB based 3D glycan structures
Links to web based Resources for Glycoconjugates
DatabaseDescription
DOUGAL Glycoprotein structures database
CabosDB Carbohydrate Sequencing Database
GlycoSuiteDB A curated database of glycoprotein glycan contains 9436 entries, sourced from 864 references, representing 245 species (Encoding IUPAC condensed)
Lectin Frontier DataBase (LfDB) carbohydrate?protein interaction data
Glyco3D 3D structures of carbohydrates, glycosyltransferases and lectins
Lectin Database A searchable database of Lectins from Algal, Animal, Bacterial, Fungal, Yeast, Plant, Virus
CFG (GBP molecules DB) A database of Glycan Binding Protein
JCGG (Lectin Frontier DB) Provides quantitative interaction data in terms between lectins and pyridylaminated (PA) glycans
Animal Lectins A genomic resource of animal lectins
O Glycbase Database of O and C linked glycoproteins
GlycoProtDB Collection of experimentally identified N-glycosylated proteins of C. elegans N2 and mouse tissues (strain C52BL/6J, male)
IUPHAR?DATABASE An annotated and expert reviewed database of Mammalian Glycoprotein hormone receptors
VSGdb A database of trypanosome variant surface glycoproteins
GlycoBase 6.0 Database of published experimental HPLC (elution profile) data for N-glycans and O-glycans
dbPTM Different databases of experimentally verified PTM are linked under dbPTM and it also provides for predicted PTM annotation on SwissProt entries
GlycoPep DB Database of N linked glycan structures derived from biologically relevant glycopeptides
SysPTM Provides for manually curated multi-type post translational modification data with four data mining tools for Proteome research
CBS CBS prediction servers - Numerous tools to analyze protein sequences, Post-translational modifications of proteins Protein function and structure:
Glycan Library? A list of approximately 830 lipid-linked sequence-defined glycan probes derived from diverse natural sources or chemically synthesised
GlycoBase 3.2? A database of over 650 N- and O- linked glycan structures HPLC, UPLC, exoglycosidase sequencing and mass spectrometry (MALDI-MS, ESI-MS, ESI-MS/MS, LC-MS, LC-ESI-MS/MS) data
EPS database Provides access to detailed structural, taxonomic and bibliographic information on bacterial exopolysaccharide structures and properties
dbCAN2 A meta server for automated carbohydrate-active enzyme annotation
GLYCAM Molecular Modelling Library?(GMML) Assists in a variety of molecular modelling tasks, with a focus on the needs of carbohydrates
CCRC Spectral Database For partially methylated alditol acetates (PMAAs)
GlycoGAIT: Glycosylation and Gut Associated Immune Tolerance A database of glycogenes and lectins under gastric inflammatory diseases
Glycoproteomics MS Tools
DatabaseDescription
Glyco-Peakfinder Tool to assist the manual interpretation of MS spectra of glycans as well as glycoconjugates
GlycoMod Prediction of possible oligosaccharide structures that occur on proteins from their experimentally determined masses
SimGlycan Glycan and glycopeptide MS/MS data analysis tool
GlycoSpectrumScan Analysis of Mass spectrum for N and O linked glycopeptides
GlycoPep ID Identifying the peptide moiety of glycopeptides generated using a nonspecific enzyme
SugarBind A web resource of pathogen lectins and their carbohydrate ligands
STAT A saccharide topology analysis tool used in combination with tandem mass spectrometry
GlycoPep Grader (GPG) A free software tool designed to analyze MS/MS data obtained for N-linked glycopeptides.
LaCyTools A Targeted Liquid Chromatography-Mass Spectrometry Data Processing Package for Relative Quantitation of Glycopeptides.
GLYCH Automated interpretation of MS/MS spectra of oligosaccharides.
pGlyco Identification of intact glycopeptides by integrating HCD-MS/MS, CID-MS/MS and MS3 information.?
GRITS Toolbox A glycomics MS data processing tool
Tools for prediction and analysis of glycosylation sites/ residues
DatabaseDescription
Big-Pi Prediction of GPI-anchors
DGPI GPI-anchor prediction
GPI-SOM Prediction of GPI-anchors
NetCGlyc Prediction of C-mannosylation
NetNGlyc Prediction of N-glycosylation
NetOGlyc Prediction of O-glycosylation
YinOYang Prediction of O-beta-GlcNAc-ylation
EnsembleGly Prediction of O-, N- and C-glycosylation
CKSAAP_OGlySite Prediction of Mucin-type O-glycosylation
GlycoDomainViewer? An online resource to study site glycosylation with respect to protein context and conservation
GPP Prediction of O- and N-glycosylation
GlySeq Statistical analysis of glycosylation sites of PDB and SwissProt entries based on sequence
GlyVicinity Statistical analysis of glycosylation sites based on 3D structures
Cartoonist Cartoonist is an automated N-glycan profiling tool that can be used to annotate the spectrum.
OGlcNAcScan O-GlcNAcylation site prediction system
FindMod Peptides with experimentally measured masses are characterized for possible modifications
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.
PGlcS Prediction of protein O-GlcNAcylation sites with multiple features and analysis.
ISOGlyP Isoform specific O-glycosylation prediction
PTM prediction-User Interface List of available PTM prediction servers
GlycoPP GlycoPP: a webserver for prediction of N- and O-glycosites in prokaryotic protein sequences
GlycoEP In silico Platform for Prediction of N-, O- and C-glycosites in Eukaryotic Protein Sequences
DictyOGlyc Scanning the available Dictyostelium discoideum proteome for O-linked GlcNAc glycosylation sites using neural networks
Oglyc Predicting O-glycosylation sites in mammalian proteins by using SVMs
SFAT Structure-based Comparative Analysis and Prediction of N-linked Glycosylation Sites in Evolutionarily Distant Eukaryotes
GlycoMine A machine learning-based approach for predicting N-, C- and O-linked glycosylation in the human proteome
GlycoMinestruct A new bioinformatics tool for highly accurate mapping of the human N-linked and O-linked glycoproteomes by incorporating structural features
StrOligo N-glycosylation algorithm
OSCAR An algorithm for assigning oligosaccharide topology from MSn data
Glycolyzer Identify a set of glycan biomarkers that highly discriminate between cases and controls
DAGR? Database of Anti-Glycan Reagents ??use to search and identify antibodies and reagent lectins to various carbohydrate
NGlycPred Server N-linked Glycosylation Prediction Server Incorporating Structural Information and Patterns
Tools for Glycoprotein Structure/ Conformation
DatabaseDescription
Glycoprotein Builder Tool to build 3D structure of oligosaccharides and in silico glycosylation of N and/ or O linked Glycoprotein
GlyProt Tool for in silico glycosylation of N linked glycoprotein
Glydict Tool for Rapid Exploration of Conformational Space of N-Glycans
pdb2linucs Detection of carbohydrate moieties in PDB structures
GlycoTorsion Statistical analysis of torsion angles derived from the PDB
Dynamic Molecules Online molecular dynamics (MD) simulations
pdb-care PDB carbohydrate residue check
Multi N-Glycan Multi N-Glycan uses pre-derived N-glycans as candidates that are created based on known N-glycan synthetic pathways
GS-align For glycan structure alignment and similarity measurement
Distance mapping Computational method to provide conformational space of oligosaccharides
SweetUnityMol Software to display 3-D structures of carbohydrates, polysaccharides and glycoconjugates
doGlycans Tools for Preparing Carbohydrate Structures for Atomistic Simulations of Glycoproteins, Glycolipids, and Carbohydrate Polymers for GROMACS
GlycoTree Used to predict the retention times of glycan structures
Glycoblocks A schematic three-dimensional representation for glycans and their interactions
GLYCAM N-glycans modeled onto it using the online portal