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Showing 20 records out of 27 total
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Categories: proteomics, glycomics - Software type(s): website - database
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.
Categories: proteomics, glycomics - Software type(s): website - database
CSDB covers information on structures and taxonomy of natural carbohydrates published in the literature and mostly resolved by nuclear magnetic resonance (NMR). CSDB is composed of two parts: Bacterial & Archeal (BCSDB) and Plant & Fungal (PFCSDB). The databases can be queried together or separately with multiple criteria. Supporting tools for NMR data analysis and prediction as well as statistical analysis of glycomes in taxa are included.
Categories: proteomics, glycomics - Software type(s): website - tool
Glycan structures submitted to EpitopeXtractor are compared to the complete collection of glycan determinants stored in the Glydin' network (http://glycoproteome.expasy.org/epitopes/). The tool extracts all matching substructures and displays them as SNFG cartoons (Symbol Nomenclature for Glycans (SNFG) described here https://www.ncbi.nlm.nih.gov/glycans/snfg.html) with the option of mapping the results on the Glydin' network.
Categories: proteomics, glycomics - Software type(s): website - tool
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.
Categories: proteomics, (protein modifications), glycomics - Software type(s): website - tool
Calculate the mass of an oligosaccharide structure.
Categories: proteomics, glycomics - Software type(s): website - database
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.
Categories: proteomics, glycomics - Software type(s): website - tool
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.
Categories: proteomics, glycomics - Software type(s): website - tool
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.
Categories: proteomics, (protein sequences and identification, proteomics experiment, protein modifications), glycomics - Software type(s): website - tool
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.
Categories: proteomics, (protein modifications), glycomics - Software type(s): website - database/tool
GlyConnect is a platform integrating several sources of information to characterise the molecular actors of glycosylation, mainly glycoproteins and N- and O-linked glycans. The purpose of GlyConnect is to bring out in a single resource the relationships between glycans, the proteins that carries them, the enzymes that synthesise or degrade them and the proteins that bind them. GlyConnect also integrates tools otherwise accessible individually in the glycomics collection of ExPASy.
Categories: proteomics, (proteomics experiment) - Software type(s): website - tool
Visualisation tool for representing a set of glycan structures as a summary figure of all structural features using icons and colours recommended by the Consortium for Functional Glycomics (CFG).
Categories: proteomics, glycomics - Software type(s): website - tool
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.
Categories: proteomics, glycomics - Software type(s): website - tool
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.
Categories: proteomics, glycomics - Software type(s): website - tool
GlyS3 matches any substructure such as glycan determinants to a large collection of structures recorded in UniCarbKB, SugarBind or GlycomeDB.
Categories: proteomics, glycomics - Software type(s): website - database
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).
Categories: proteomics, (function analysis), glycomics - Software type(s): website - database
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.
Categories: proteomics, (protein modifications), glycomics - Software type(s): website - tool
Neural network predictions of C-mannosylation sites in mammalian proteins.
Categories: proteomics, (protein modifications), glycomics - Software type(s): website - tool
NetNGlyc predicts N-Glycosylation sites in human proteins using artificial neural networks that examine the sequence context of Asn-Xaa-Ser/Thr sequons.
Categories: proteomics, (protein modifications), glycomics - Software type(s): website - tool
Neural network predictions of mucin type GalNAc O-glycosylation sites in mammalian proteins.
Categories: proteomics, glycomics - Software type(s): website - tool
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.
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