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Showing 20 records out of 372 total
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Categories: proteomics, (protein structure) - Software type(s): website - tool
Geno3D is an automatic web server for protein molecular modelling
Categories: systems biology - Software type(s): CLI, GUI - tool
A tool to extract duplicate genes and their amino acid and synonymous divergence from completely sequenced genomes.
keywords:
Categories: systems biology, evolutionary biology - Software type(s): website - tool
A genotype network is a graph in which vertices represent genotypes that have the same phenotype. The Genonets Server is a tool that provides the following features: (i) the construction of genotype networks for categorical and univariate phenotypes from DNA, RNA, amino acid or binary sequences; (ii) analyses of genotype network topology and how it relates to robustness and evolvability, as well as analyses of genotype network topography; (iii) multiple interactive visualizations.
keywords: network
Categories: proteomics, (protein structure) - Software type(s): website - tool
GlobPlot is a web service that allows the user to plot the tendency within the query protein for order/globularity and disorder
Categories: 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: glycomics - Software type(s): website - tool
Exoglycosidase cleavage of monosaccharides results in signature peak shifts, in both UPLC and MS1. Manual interpretation of exoglycosidase data is complex and time consuming. GlycanAnalyzer is a web application that pattern matches N-glycan peak shifts following exoglycosidase digestion and automates structure assignments. GlycanAnalyzer significantly improves assignment accuracy over other auto-assignment methods on tests with a monoclonal antibody.
Categories: glycomics - Software type(s): website - tool
Calculate the mass of an oligosaccharide structure.
Categories: 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: 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, 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: glycomics - Software type(s): website - database
GlycoPedia collects e-chapters on basic, intermediary and advanced topics of glycoscience. It also compiles various sources and suggests relevant readings to the scientific community.
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: glycomics - Software type(s): website - tool
GlyCosmos is a Web portal for omics data pertaining to the glycosciences. Based on Semantic Web technologies, data in Resource Description Framework (RDF) are stored in a publicly available SPARQL endpoint, and user interfaces are provided to easily browse and search this data. Repositories pertaining to glycans (GlyTouCan), glycomics data (GlycoPOST) and glycoconjugates (GlyComb) are available, as well as entry points for genes, proteins, lipids, pathways, diseases and glycomes.
keywords: glycomics
Categories: glycomics - Software type(s): website - database
GlycoStore is a curated chromatographic, electrophoretic and mass-spectrometry composition database of N-, O-, glycosphingolipid (GSL) glycans and free oligosaccharides associated with a range of glycoproteins, glycolipids and biotherapeutics. The database is built on publicly available experimental data sets from GlycoBase (NIBRT, Ireland), Bioprocessing Technology Institute (BTI) A*STAR, Macquarie University and Ludger Ltd.
Categories: 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 structurally related glycan sub-structures.
Categories: glycomics - Software type(s): website - database
GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data. GlyGen retrieves information from multiple international data sources and integrates and harmonizes this data. GlyGen also provides machine readable APIs and a SPARQL endpoint to access the integrated data.
keywords: glycomics
Categories: 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: glycomics - Software type(s): website - tool
GlyS3 matches any substructure such as glycan determinants to a large collection of structures recorded in Glyconnect or SugarBind.
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