Related Tools & Database
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List the other available tools and databases related to glycoproteins and glycosyltransferases.
| Database | Description |
|
Databases and Tools | |
| 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 |
| IUPHAR DATABASE | An annotated and expert reviewed database of Mammalian Glycoprotein hormone receptors |
| BRENDA | Repository of Enzyme Information |
| STRING | Database of known and predicted protein interactions |
| Lectin Frontier DataBase (LfDB) | carbohydrate–protein interaction data |
| Animal Lectins | A genomic resource of animal lectins |
| BCSDB | Structural, bibliographic, taxonomic and related information on bacterial carbohydrate structures (Encoding BCSDB linear code) |
| CAZy | Carbohydrate active enzymes |
| 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. |
| JCGGDB | Database of Glyco genes, glycoproteins, lectin affinity, MS data, epitopes (Encoding CabosML) |
| EUROCarbDB | European Depository and Portal for carbohydrate (Encoding GlycoCT) |
| GLYCOSCIENCES.de | Collection of tools and databases for glycobiology Encoding (LINUCS) |
| Glyco3D | 3D structures of carbohydrates, glycosyltransferases and lectins |
| Lectin Database | A searchable database of Lectins from Algal, Animal, Bacterial, Fungal, Yeast, Plant, Virus |
| EPS database | Provides access to detailed structural, taxonomic and bibliographic information on bacterial exopolysaccharide structures and properties |
| GlycoPep DB | Database of N linked glycan structures derived from biologically relevant glycopeptides |
| KEGG Pathway Database | Carbohydrate metabolism pathways |
| UniCarb-DB | continuation of the EUROCarbDB, repository for Glycan mass spectrometric data and structural assignment based on fragmentation data |
| GlycoGene Database (GGDB | A database of human genes associated with glycan synthesis such as glycosyltransferase, sugar nucleotide synthases etc |
| GlycoMapsDB | Conformational maps of carbohydrates |
| GlycoStore | A database of retention properties for glycan analysis |
| GlycoepitopeDB | Database of carbohydrate recognition motifs, recognising anti-bodies and glycoproteins/glycolipids carrying the motifs |
| Elution Coordinate DB | Database of 2-aminopyridine labelled glycans |
| 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 |
| 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 |
| MCAW-DB | A glycan profile database capturing the ambiguity of glycan recognition patterns. |
| GlycoPep DB | MS glycan analysis tool |
| GlycoSuiteDB | A curated database of glycoprotein glycans. |
| GlyTouCan | International glycan structure repository that assigns globally unique accession numbers to any glycan |
|
Links to web based resources for carbohydrates | |
| RINGS | Resource for Informatics of Glycomes at Soka |
| Glycan | A database of PDB-based glycan 3D structures |
| 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 |
| dbCAN | A web server and DataBase for automated Carbohydrate-active enzyme Annotation |
|
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 |
| 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 |
|
NMR Tools | |
| GlyNest | Estimation of NMR chemical shifts |
| CCPN | Website of the Collaborative Computing Project for NMR |
|
Glycan structure/conformation Tool | |
| 3D SNFG | Generates 3D shapes of glycans that match the SNFG format (Symbol Nomenclature for Glycans) |
|
Links to web based Resources for Glycoconjugates | |
| Glycan Library | A list of approximately 830 lipid-linked sequence-defined glycan probes derived from diverse natural sources or chemically synthesised |
| dbCAN2 | A meta server for automated carbohydrate-active enzyme annotation |
|
Glycoproteomics MS Tools | |
| pGlyco | Identification of intact glycopeptides by integrating HCD-MS/MS, CID-MS/MS and MS3 information. |
| GRITS Toolbox | A glycomics MS data processing tool |
| SimGlycan | Glycan and glycopeptide MS/MS data analysis tool |
|
Tools for prediction and analysis of glycosylation sites/ residues | |
| GPI-SOM | Prediction of GPI-anchors |
| GPP | Prediction of O- and N-glycosylation |
| 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. |
| 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 |
| GlycoMinestruct | A new bioinformatics tool for highly accurate mapping of the human N-linked and O-linked glycoproteomes by incorporating structural features |
| 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 | |
| Dynamic Molecules | Online molecular dynamics (MD) simulations |
| GS-align | For glycan structure alignment and similarity measurement |
| 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 |
| GLYCAM | N-glycans modeled onto it using the online portal |