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Databases and Tools Cross-Referenced in ProGlyProtdb
Database Description
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
3DJIGSAW This server builds three-dimensional models for proteins based on homologues of known structure
Seqlogos Server uses the DALILA package to create sequence logos from input files derived from sequence alignments using a perl script
Links to web based Resources for Carbohydrates
Major Carbohydrate Portals, Databases and Tools
Carbohydrate Portals and Databases Description
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 databse 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
MS Tools Description
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
NMR Tools Description
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 ComputingP roject for NMR
HPLC Tools Description
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
Glycan structure/conformation Tool Description
Sweet-II Generation of 3D carbohydrate structure models
Glycan Builder Visual editor of glycan structure
Carbohydrate 3D Structure Predictor Tool to create 3D glycan structure from linear sequences
CARP Carbohydrate Ramachandran Plot
DrawRINGS Tool for 2D glycan structure Drawings
GlycoMaps DB Conformational maps
Disaccharides Conformational maps
Links to web based Resources for Glycoconjugates
Major Glycoprotein & Lectin Databases and Tools
Glycoprotein & Lectin Databases Description
DOUGAL Glycoprotein structures database
GlycoSuiteDB A curated database of glycoprotein glycan contains 9436 entries, sourced from 864 references, representing 245 species (Encoding IUPAC condensed)
Glyco3D 3D structures of carbohydrates, glycosyltransferases and lectins
Lectin Database A searchable databse 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 indentified 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 Databse 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
GlycoFly A database for Drosophila N-linked glycopeptides (721 unique peptides) detected using Mass spectroscopy
GlycoFish A database of N-linked glycopeptides (265 unique glycopeptides) of Zebrafish (Danio rerio) identified using mass spectroscopy
Glycoproteomics MS Tools Description
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
Tools for prediction and analysis of glycosylation sites/ residues
Tool Description
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
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
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.
PTM prediction-User Interface list of available PTM prediction servers
Glycoprotein Structure/ Conformation tools
Tool Description
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
GlyTorsion Statistical analysis of torsion angles derived from the PDB
Dynamic Molecules Online molecular dynamics (MD) simulations
pdb-care 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.
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