RibAlign is a tool for scientists who are interested in phylogenetic reconstructions based on concatenated ribosomal protein sequences of Bacteria (no Archaea at this time). Basically, RibAlign serves two purposes: First, it provides a fast and scalable database that has been specifically adapted to ribosomal protein sequences and second, it provides sophisticated import and export capabilities. This includes semi-automatic extraction of ribosomal protein sequences from whole-genome GenBank and FASTA files as well as producing aligned exports that can directly be used in conjunction with the PHYLIP and the MrBayes phylogenetic reconstruction programs. ... [Information of the supplier]
The Dali server is a network service for comparing protein structures in 3D. You submit the coordinates of a query protein structure and Dali compares them against those in the Protein Data Bank. A multiple alignment of structural neighbours is emailed back to you. In favourable cases, comparing 3D structures may reveal biologically interesting similarities that are not detectable by comparing sequences. If you want to know the structural neighbours of a protein already in the Protein Data Bank (PDB), you can find them in the Dali Database. The Dali Domain Dictionary is a numerical taxonomy of all known structures in the PDB - you can view the entire Dali classification by following the link to the Dali Domain Dictionary. ... [Information of the supplier]
SEVENS summarizes GPCR (G-protein coupled receptor) genes that are identified with high accuracy from 56 eukaryote genomes, by a pipeline integrating such software as a gene finder, a sequence alignment tool, a motif and domain assignment tool, and a transmembrane helix predictor. This treats a larger data space (than that in currently available other databases), which should include not only the expressed sequences but also the newly identified sequences that cannot be detected by in vivo experiments, although they definitely exist on the genome sequence and are just waiting for the opportunity to express their functions. SEVENS can provides the infrastructure of general information of "GPCR universe" for comparative genomics. ... [Information of the supplier]
PTMCode is a resource of known and predicted functional associations between protein posttranslational modifications (PTMs). It currently contains 13 different PTM types in proteins from 8 different eukaryotic species. A total of 137525 sites and 401688 functional associations in 25764 proteins can currently be explored. ... [Information of the supplier]
dcGO is a comprehensive ontology database for protein domains. Domains are often the functional units of proteins, thus instead of associating ontological terms only with full-length proteins, it sometimes makes more sense to associate terms with individual domains. Domain-centric GO, "dcGO", provides associations between ontological terms and protein domains at the superfamily and family levels. Some functional units consist of more than one domain acting together or acting at an interface between domains; therefore, ontological terms associated with pairs of domains, triplets and longer supra-domains are also provided. At the time of writing the ontologies in dcGO include the Gene Ontology (GO); Enzyme Commission (EC) numbers; pathways from UniPathway; human phenotype ontology and phenotype ontologies from five model organisms, including plants; anatomy ontologies from three organisms; human disease ontology and drugs from DrugBank. All ontological terms have probabilistic scores for their associations. In addition to associations to domains and supra-domains, the ontological terms have been transferred to proteins, through homology, providing annotations of >80 million sequences covering 2414 complete genomes, hundreds of meta-genomes, thousands of viruses and so forth. The dcGO database is updated fortnightly, and its website provides downloads, search, browse, phylogenetic context and other data-mining facilities. Source of abstract: Hai Fang and Julian Gough 2013 in Nucl. Acids Res. 41, DB Issue -CC-BY-NC 3.0 ... [Miscellaneous as indicated]
ModBase is a database of comparative protein structure models, calculated by our modeling pipeline ModPipe. ModBase contains theoretically calculated models, not experimentally determined structures. The models may contain significant errors. [Information of the supplier, modified]
This website provides a current list of membrane protein structures determined by x-ray and electron diffraction with links to the Protein Data Bank and other useful sites. Although this database emphasizes structures determined by diffraction methods, some NMR structures are included as well. [Information of the supplier, modified]