Databases and Tools Cross Referred in ProGlycProt
Database
Description
National Center for Biotechnology
Information
PubMed
NCBI Taxonomy Browser
Genbank
EMBL
Nucleotide
Resource for Biomedical and Genomic information
EMBL-CDS
UniProtKB (Protein knowledgebase)
RCSB PDB
BRENDA
STRING
BCSDB
CAZy
Literature Resource
Database of Taxonomic Information
Nucleotide Sequence database
Nucleotide Sequence Database
Database of sequences from several sources, including GenBank, RefSeq, TPA and
PDB. Genome, gene and transcript sequence data
Nucleotide Sequence database of Coding Sequences features
Resource of protein sequence and functional information
Database of Protein structures
Repository of Enzyme Information
Database of known and predicted protein interactions
Structural, bibliographic, taxonomic and related information on bacterial
carbohydrate structures (Encoding BCSDB linear code)
Carbohydrate active enzymes
Links to web based Resources for Carbohydrates
Major Carbohydrate Portals, Databases and Tools
Carbohydrate Portals and Databases
Content
JCGGDB
Elution Coordinate DB
GlycomeDB
MonoSaccharideDB
Database of Glyco genes, glycoproteins, lectin affinity, MS data, epitopes (Encoding
CabosML)
Websites of the Consortium for Functional Glycomics. Databases of Glycans,
lectins, glycosyltransferases (Encoding Glycominds Linear Code)
Resource for Carbohydrate related literature, networks and structures
European Depository and Portal for carbohydrate (Encoding GlycoCT)
Collection of tools and databases for glycobiology Encoding (LINUCS)
Resource for Informatics of Glycomes at Soka
Complex Carbohydrate Structure Database, first &largest carbohydrate database
with 50 000 records of around 15 000 different carbohydrate structures (encoding
IUPAC extended)
collection of experimentally determined glycan structures (Encoding KCF )
continuation of the EUROCarbDB, repository for Glycan mass spectrometric data
and structural assignment based on fragmentation data
Carbohydrate-NMR database that combines CarbBank data with chemical shift
values
Conformational maps of carbohydrates
Conformational maps of disaccharides
Carbohydrate metabolism pathways
Bacterial Polysaccharide Gene Database
KEGG Orthology (KO) groups for glycosyltransferases
A database of human genes associated with glycan synthesis such as
glycosyltransferase, sugar nucleotide synthases etc
A databse of GTs
3D structure database of glycosyltransferases
Database of carbohydrate recognition motifs, recognising anti-bodies and
glycoproteins/glycolipids carrying the motifs
Database of enzymes for biosynthesis of GPI anchors
Database of 2-aminobenzamide labelled N glycan structures and exoglycosidase
digestion pathways
Database of 2-aminopyridine labelled glycans
Meta-database to search various databases via one interface
Reference database for monosaccharide notation
MS Tools
Description
GlycoWorkbench
Tool for drawing of glycan structures based on glycan composition determined from
their mass spectrometry data
Determination of glycan composition from their mass signal
Tool for annotation of Glycan MS spectra
CFG
Glycoconjugate Data Bank
EUROCarbDB
GLYCOSCIENCES.de
RINGS
CCSDB/CarbBank
KEGG Glycan
UniCarb-DB
Sugabase
GlycoMapsDB
DisaccharideDB
KEGG Pathway Database
BPGD
KEGG Orthology Database
GlycoGene Database (GGDB
CFG glycosyltransferase database
CERMAV glycosyltransferase database
GlycoepitopeDB
GPI Anchor Biosynthesis Report
GlycoBase
Glyco-Peakfinder
GlycoPep DB
GlycoMiner
Glycofragment
GlycosidIQ
MS glycan analysis tool
Composition analysis of N glycan chain linked to a protein
Calculate and display the main fragments (Band C-, Z- and Y-, A- and X-ions) of
oligosaccharides that should occur in MS spectra
Calculation of the mass of an oligosaccharide structure from its composition
Search GLYCOSCIENCES.de database for structures matching a given set of MS
mass peaks
Tool for fast annotation of glycan MS spectra, results can be used for advanced
database search in GLYCOSCIENCES.de
Glycofragment mass fingerprinting
NMR Tools
Description
CASPER
GlyNest
ProSpectND
CCPN
Simulation of NMR spectra and carbohydrate sequence determination from NMR
chemical shift values
Estimation of NMR chemical shifts
Integrated NMR data processing and inspection tool
Website of the Collaborative ComputingP roject for NMR
HPLC Tools
Description
autoGU
GALAXY
GlycoExtractor
Tool to assist the interpretation of HPLC data
Visualization of HPLC 2-D maps
Automatic extraction of experimental HPLC data for multiple samples in various
downstream analysis compatible formats
Glycan structure/conformation Tool
Description
Sweet-II
Glycan Builder
Carbohydrate 3D Structure Predictor
CARP
DrawRINGS
GlycoMaps DB
Disaccharides
Generation of 3D carbohydrate structure models
Visual editor of glycan structure
Tool to create 3D glycan structure from linear sequences
Carbohydrate Ramachandran Plot
Tool for 2D glycan structure Drawings
Conformational maps
Conformational maps
GlycanMass
GlycoSearchMS
GlycoPeakfinder
Links to web based Resources for Glycoconjugates
Major Glycoprotein & Lectin Databases and Tools
Glycoprotein & Lectin Databases
Description
DOUGAL
GlycoSuiteDB
Glyco3D
Lectin Database
CFG (GBP molecules DB)
JCGG (Lectin Frontier DB)
Animal Lectins
O Glycbase
GlycoProtDB
IUPHAR DATABASE
VSGdb
GlycoBase 6.0
dbPTM
GlycoPep DB
SysPTM
Glycoprotein structures database
A curated database of glycoprotein glycan contains 9436 entries, sourced from 864
references, representing 245 species (Encoding IUPAC condensed)
3D structures of carbohydrates, glycosyltransferases and lectins
A searchable databse of Lectins from Algal, Animal, Bacterial, Fungal, Yeast, Plant,
Virus
A database of Glycan Binding Protein
Provides quantitative interaction data in terms between lectins and pyridylaminated
(PA) glycans
A genomic resource of animal lectins
Database of O and C linked glycoproteins
Collection of experimentally indentified N-glycosylated proteins of C. elegans N2
and mouse tissues (strain C52BL/6J, male)
An annotated and expert reviewed database of Mammalian Glycoprotein hormone
receptors
A database of trypanosome variant surface glycoproteins
Database of published experimental HPLC (elution profile) data for N-glycans and
O-glycans
Different databases of experimentally verified PTM are linked under dbPTM and it
also provides for predicted PTM annotation on SwissProt entries
Databse of N linked glycan structures derived from biologically relevant
glycopeptides
Provides for manually curated multi-type post translational modification data with
four data mining tools for Proteome research
Glycoproteomics MS Tools
Description
Glyco-Peakfinder
Tool to assist the manual interpretation of MS spectra of glycans as well as
glycoconjugates
Prediction of possible oligosaccharide structures that occur on proteins from their
GlycoMod
experimentally determined masses
SimGlycan
GlycoSpectrumScan
GlycoPep ID
Tool
Glycan and glycopeptide MS/MS data analysis tool
Analysis of Mass spectrum for N and O linked glycopeptides
Identifying the peptide moiety of glycopeptides generated using a nonspecific
enzyme
Tools for prediction and analysis of glycosylation sites/ residues
Description
Big-Pi
DGPI
GPI-SOM
NetCGlyc
NetNGlyc
NetOGlyc
YinOYang
EnsembleGly
CKSAAP_OGlySite
GPP
GlySeq
GlyVicinity
FindMod
GECS
PTM prediction-User Interface
Tool
Glycoprotein Builder
GlyProt
Glydict
pdb2linucs
GlyTorsion
Dynamic Molecules
pdb-care
Prediction of GPI-anchors
GPI-anchor prediction
Prediction of GPI-anchors
Prediction of C-mannosylation
Prediction of N-glycosylation
Prediction of O-glycosylation
Prediction of O-beta-GlcNAc-ylation
Prediction of O-, N- and C-glycosylation
Prediction of Mucin-type O-glycosylation
Prediction of O- and N-glycosylation
Statistical analysis of glycosylation sites of PDB and SwissProt entries based on
sequence
Statistical analysis of glycosylation sites based on 3D structures
Peptides with experimentally measured masses are characterized for possible
modifications
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.
list of available PTM prediction servers
Glycoprotein Structure/ Conformation tools
Description
Tool to build 3D structure of oligosaccharides and in silico glycosylation of N and/
or O linked Glycoprotein
Tool for in silico glycosylation of N linked glycoprotein
Tool for Rapid Exploration of Conformational Space of N-Glycans
Detection of carbohydrate moieties in PDB structures
Statistical analysis of torsion angles derived from the PDB
Online molecular dynamics (MD) simulations
PDB carbohydrate residue check
References:
 Frank, M. and S. Schloissnig (2010). "Bioinformatics and molecular modeling in glycobiology." Cell Mol Life Sci
67(16): 2749-72.
 Lutteke, T. (2008). "Web resources for the glycoscientist." Chembiochem 9(13): 2155-60.
 Marchal, I., G. Golfier, et al. (2003). "Bioinformatics in glycobiology." Biochimie 85(1-2): 75-81.
 von der Lieth, C. W., A. Bohne-Lang, et al. (2004). "Bioinformatics for glycomics: status, methods, requirements
and perspectives." Brief Bioinform 5(2): 164-78.
 von der Lieth, C. W., T. Lutteke, et al. (2006). "The role of informatics in glycobiology research with special
emphasis on automatic interpretation of MS spectra." Biochim Biophys Acta 1760(4): 568-77.