Related Tools & Database
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List the other available tools and databases related to glycoproteins and glycosyltransferases.
| Database | Description |
|
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 |
| GLYCOSCIENCES.de | 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 |