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SugarBindDB / SugarBind Database
Covers knowledge of glycan binding of human pathogen lectins and adhesins. SugarBindDB is a curated database; each glycan-protein binding pair is associated with at least one published reference. The core data element of SugarBindDB is a set of three inseparable components: the pathogenic agent, a lectin/adhesin and a glycan ligand. Each entity (agent, lectin or ligand) is described by a range of properties that are summarized in an entity-dedicated page. Several search, navigation and visualisation tools are implemented to investigate the functional role of glycans in pathogen binding. The database is cross-linked to protein and glycan-related resources such as UniProtKB and UniCarbKB.
EK3D / E. coli K antigen 3-Dimensional Structure Database
A repository of 72 E. coli K antigens that provides information about sugar compositions, their anomeric and enantiomeric forms and linkages between the sugar monomers. The database also has the collection of 3D structural models of the K antigen repeating units that are derived from the above information. As the classification of E. coli into group 1, 2, 3 and 4 is developed based on K antigens, the database also contains information about the group based serotyping of E. coli K antigens. As the capsules are molecules of 100–10000 kD multimers, the database also provides the facility to generate polymeric structures of K antigen repeat units.
A mass spectrometry-based glycoproteomic characterization of zebrafish embryos was performed to identify the N-linked glycoproteins and N-linked glycosylation sites. To increase the number of glycopeptides, proteins from zebrafish were digested with two different proteases--chymotrypsin and trypsin--into peptides of different length. The N-glycosylated peptides of zebrafish were then captured by the solid-phase extraction of N-linked glycopeptides (SPEG) method and the peptides were identified with an LTQ OrbiTrap Velos mass spectrometer.
Provides a list of all available experimental information on agl (archaeal glycosylation) genes and proteins. Aglgenes offers a web interface that does not requires any particular training. It includes a single search field that allows user to search through all published experimental data on genes and proteins involved in archaeal N-glycosylation. This database allows users to submit updates on existing entries or new information on archaeal N-glycosylation pathway components.
Assists data interpretation to bring glycan analysis within the reach of any well-established laboratory. GlycoBase provides an open-access relational database of glycan structures and primary research data, accessed via a web-based interface. It was designed to support HILIC 2-aminobenzamide (2AB) approaches with an open-source philosophy intended to enhance software development, data management, and to progress the application of glycoinformatics in glycomics and glycoproteomics.
GlycoGAIT / Glycosylation and Gut Associated Immune Tolerance
Identifies glycosylation relevance in gut barrier in response to commensal and pathogenic bacteria for modulating the gut immune tolerance. The GlycoGAIT is a web database whose interface enables the users to quickly compare or interpret changes in expression patterns of glycome genomics below different gut associated inflammatory conditions. This tool delivers informations for glycogene expression analysis under inflammatory disease conditions. It brings also the gene set of glycogenes along with lectins along with publically available gene expression data obtained from human gastric biopsy samples with dysregulated immune function that aids in the systematic analysis of the gene expression changes in disease conditions at the transcriptome level.
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