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Databases

  • CAZy  •  CAZy is a dedicated family classification system correlating structure and molecular mechanism of carbohydrate-active enzymes. It describes the families of structurally-related catalytic and carbohydrate-binding modules (or functional domains) of enzymes that degrade, modify, or create glycosidic bonds.  [less]
  • Glyco3D  •  A single entry portal to access three-dimensional features of (1) carbohydrate and carbohydrate polymers in different physical and biological conditions, a nd (2) carbohydrate-binding proteins crystallised with their carbohydrate ligands (lectins, monoclonal antibodies, glycosyltransferases). Most data is structural data arising from diffraction experiments, but three-dimensional models resulting from theoretical calculations are also included. 3D structures can be viewed across the website. [less]
  • GlyTouCan  •  GlyTouCan is the international glycan structure repository. It is an uncurated registry for glycan structures that assigns globally unique accession numbers to any glycan independent of the level of information provided by the experimental method used to identify the structure(s). [less]
  • MatrixDB  •  MatrixDB is a curated database of interactions between extracellular matrix proteins, proteoglycans and polysaccharides. It mainly focuses on protein-glycosaminoglycan (GAG) interactions, as GAGs are complex and abundant polysaccharides in the ECM and at the cell surface, where they play key roles in adhesion and signaling.  [less]
  • SugarBind  •  SugarBind covers knowledge of glycan binding of human pathogen lectins and adhesins. Information is collected by experts from articles published in peer-reviewed scientific journals. The data were compiled through an exhaustive search of literature published over the past 30 years by glycobiologists, microbiologists, and medical histologists.  [less]
  • UniCarb-DB  •  UniCarb-DB stores data and information on glycan structures and associated fragment data characterised by LC-MS/MS strategies. It is annotated with high-quality datasets. [less]
  • UniCarbKB  •  UniCarbKB is a curated and annotated glycan database which curates information from the scientific literature on glycoprotein derived glycan structures. It includes data previously available from GlycoSuiteDB. [less]

Tools

  • GLYCAM-Web  •  The tools at GLYCAM-Web automate the prediction of 3D structures of glycans, glycosaminoglycans, and glycoproteins, and provide all files necessary for the user to perform molecular dynamics simulations of these systems with the AMBER software package. Additional tools facilitate the prediction of the specificity of glycan binding proteins, such as lectins and antibodies, and provide theoretical 3D structures for these complexes.  [less]
  • GlycanMass  •  Calculate the mass of an oligosaccharide structure. [less]
  • GlycoDigest  •  GlycoDigest is a tool that simulates the action of these exoglycosidases on released oligosaccharides. It assists glycobiologists in designing enzyme mixtures that can be used to guide the precise determination of glycan structures. [less]
  • GlycoDomain Viewer  •  The GlycoDomain Viewer is a tool for the visualisation of glycosylation sites in the context of the protein and conserved domains. It contains O-glycoproteomic data from the Clausen lab, and predictions of GalNAc-type glycosylation for the human proteome. [less]
  • GlycoMod  •  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. [less]
  • GlycoSiteAlign  •  GlycoSiteAlign selectively aligns amino acid sequences surrounding glycosylation sites (by default, 20 positions on each side of the glycosylated residue) depending on structural properties of the glycan attached to the site. These properties are either general (e.g., "fucosylated") or specific, such as precise composition, and are proposed in a drop-down list.  [less]
  • Glydin'  •  Glydin' compiles and maps information relative to glycoepitopes (glycan determinants) as published in the literature or reported in databases. The output is an interactive network of strucutrally related glycan sub-structures. [less]
  • Glynsight  •  Glynsight is a web interface to upload, visualize and interactively compare glycan expression profiles. The tool can process N- or O-linked glycan expression data. [less]
  • GlyS3  •  GlyS3 matches any substructure such as glycan determinants to a large collection of structures recorded in UniCarbKB, SugarBind or GlycomeDB. [less]
  • MzJava  •  MzJava is an open-source Java library for the analysis of mass spectrometry data. It provides algorithms and data structures for processing mass spectra and their associated biological molecules, such as small molecules, glycans, proteins, and peptides with post-translational modifications. MzJava includes methods to perform mass calculation, protein digestion, peptide and glycan fragmentation, MS/MS signal processing, and scoring for spectra-spectra and peptide/glycan-spectra matches.  [less]
  • NetCGlyc  •  Neural network predictions of C-mannosylation sites in mammalian proteins.  [less]
  • NetNGlyc  •  NetNGlyc predicts N-Glycosylation sites in human proteins using artificial neural networks that examine the sequence context of Asn-Xaa-Ser/Thr sequons.  [less]
  • NetOGlyc  •  Neural network predictions of mucin type GalNAc O-glycosylation sites in mammalian proteins. [less]
  • O-Glycologue  •  Built from a model of the de novo biosynthesis of O-linked glycans, O-Glycologue is a method for generating networks of reactions based on the activities of a set of 26 human glycosyltransferase and sulfotransferase enzymes. The effects of enzyme knock-outs on the network can be predicted, and also the enzymes required to produce a given O-glycan.  [less]
  • PepSweetener  •  PepSweetener supports the manual annotation of MS data for intact glycopeptides. It displays an interactive map of all theoretical glycopeptides that match the molecular masses of queried precursor ions. Ion matching can be performed in two modes: simple when the search space spans the combination of all tryptic peptides including N-glycosites in the human proteome, and advanced when the search space is custom-built by specifying peptides and glycans. [less]
  • Swiss Mass Abacus  •  Swiss Mass Abacus is a calculator of peptide and glycopeptide masses. It is purposefully kept as simple as a basic calculator executing arithmetic operations. [less]
  • YinOYang  •  The YinOYang WWW server produces neural network predictions for O-beta-GlcNAc attachment sites in eukaryotic protein sequences. This server can also use NetPhos, to mark possible phosphorylated sites and hence identify "Yin-Yang" sites.  [less]