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Showing 14 records out of 14 total

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 - tool
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.
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, (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, (proteomics experiment), glycomics - Software type(s): CLI, API - tool
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.
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, GUI - tool
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.
Categories: proteomics, (protein modifications), glycomics - Software type(s): website - database
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.
Categories: proteomics, (protein modifications), glycomics - Software type(s): website - tool
Swiss Mass Abacus is a calculator of peptide and glycopeptide masses. It is purposefully kept as simple as a basic calculator executing arithmetic operations.
Categories: proteomics, (protein modifications), glycomics - Software type(s): website - database
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.
Categories: proteomics, (protein modifications), glycomics - Software type(s): website - tool
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.