Ubiquitin-mediated signalling databases | Protein interaction data analysis
Post-translational modification of cellular proteins by ubiquitin is a pivotal regulatory event that controls not only protein degradation, but also a variety of non-proteolytic functions. Ubiquitination is involved in a broad array of physiological processes, and its dysregulation has been associated with many human diseases, including neuronal disorders and cancers. Ubiquitin-mediated signalling has thus come to the forefront of biomedical research.
Describes the network of Arabidopsis proteins responsible for the covalent attachment of ubiquitin (Ub). PlantsUBQ provides comprehensive information on the role of this post-translational modification in plants that ultimately can be used to devise new strategies to improve crop productivity.
A family-based database for ubiquitin and ubiquitin-like conjugation, which is one of the most important post-translational modifications responsible for regulating a variety of cellular processes, through a similar E1 (ubiquitin-activating enzyme)-E2 (ubiquitin-conjugating enzyme)-E3 (ubiquitin-protein ligase) enzyme thioester cascade. The detailed annotations and classifications were also provided.
A web-based database for the ubiquitination system in Saccharomyces cerevisiae (Baker's yeast). SCUD aims to represent a comprehensive yeast ubiquitination system, and is easily expandable with the further experimental data. We expect that this database will be useful for the research on the ubiquitination systems of other higher organisms.
A knowledge base of ubiquitylated proteins. UbiProt contains retrievable information about overall characteristics of a particular protein, ubiquitylation features, related ubiquitylation and de-ubiquitylation machinery and literature references reflecting experimental evidence of ubiquitylation. UbiProt can serve as a general reference source both for researchers in ubiquitin field and those who deal with particular ubiquitylated proteins which are of their interest.
Provides a comprehensive collection of available E3-substrate specificities and a systematic framework for the analysis of E3-mediated regulatory networks of diverse cellular functions. Currently, E3Net contains 2201 E3s and 4,896 substrates in 427 organisms and 1,671 E3-substrate specific relations between 493 E3s and 1,277 substrates in 42 organisms, extracted mainly from MEDLINE abstracts and UniProt comments with an automatic text mining method and additional manual inspection and partly from high throughput experiment data and public ubiquitination databases.
Offers users an effective platform to efficiently study protein ubiquitylation networks among large-scale ubiquitylation data. The current version of UbiNet was designed specifically for humans to serve as not only a meaningful framework for E3-substrate regulatory networks but also a new scheme to discover potential E3 ligases for ubiquitylated substrates. To date, UbiNet has accumulated 43 948 experimentally verified ubiquitylation sites from 14 692 ubiquitylated proteins of humans.
A public resource for the retrieval of experimentally verified human ubiquitination enzymes and substrates. hUbiquitome is the first comprehensive database of human ubiquitination cascades. Currently, hUbiquitome has in its repertoire curated data comprising 1 E1 enzyme, 12 E2 enzymes, 138 E3 ligases or complexes, 279 different substrate proteins and 17 deubiquitination enzyme terms. The biological functions of substrates from different kinds of E3s were analyzed using the collected data.
A database of higher plants' ubiquitin 26S/proteasome system (UPS). Both automated search and manual curation were performed in identifying candidate genes. Extensive annotations referring to each gene were generated, including basic gene characterization, protein features, GO (gene ontology) assignment, microarray probe set annotation and expression data, as well as cross-links among different organisms. A chromosome distribution map, multi-sequence alignment, and phylogenetic trees for each species or gene family were also created. A user-friendly web interface and regular updates make plantsUPS valuable to researchers in related fields.
Provides a scientific community with a comprehensive, freely and high-quality accessible resource of mammalian protein ubiquitination sites. The mUbiSiDa was designed to be a widely used tool for biologists and biomedical researchers with a user-friendly interface, and facilitate the further research of protein ubiquitination, biological networks and functional proteomics. It can also provide blast function to predict novel protein ubiquitination sites in other species by blast the query sequence in the deposit sequences.
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