DOLOP provides information for several hundred lipoproteins with relevant links to molecular details. Features include functional classification, predictive algorithm for query sequences, primary sequence analysis and lists of predicted lipoproteins ... [Information of the supplier, modified]
The membrane organization and subcellular location of a protein can provide information about its functional role. Historically, these data have been difficult to produce on a large scale for higher eukaryotic organisms. However, recent advances in membrane organization prediction methods and high-throughput subcellular localization assays have made it possible to generate these datasets. LOCATE is a curated, web-accessible database that houses data describing the membrane organization and subcellular localization of proteins from the FANTOM3 Isoform Protein Sequence set. Membrane organization is predicted by the high-throughput, computational pipeline MemO. The subcellular locations of selected proteins from this set were determined by a high-throughput, immunofluorescence-based assay and by manually reviewing over 1700 peer-reviewed publications. The results of the MemO pipeline and the subcellular localization methods are stored in the database with supporting information including a graphical depiction of the membrane organization juxtaposed with InterPro-predicted features and links to several external databases. The database is searchable by subcellular location, protein class, descriptive keyword, and sequence similarity. The data are retrievable in human- and machine-readable formats and in batch. ... [Information of the supplier]
The Membrane Protein Data Bank (MPDB) is an online, searchable, relational database of structural and functional information on integral, anchored and peripheral membrane proteins and peptides. Data originates from the Protein Data Bank and other databases, and from the literature. Structures are based on X-ray and electron diffraction, nuclear magnetic resonance and cryoelectron microscopy. The MPDB is searchable online by protein characteristic, structure determination method, crystallization technique, detergent, temperature, pH, author, etc. Record entries are hyperlinked to the PDB and Pfam for viewing sequence, three-dimensional structure and domain architecture, and for downloading coordinates. Links to PubMed are also provided. ... [Information of the supplier]
Organs and organelles represent core biological systems in mammals, but the diversity in protein composition remains unclear. Here, we combine subcellular fractionation with exhaustive tandem mass spectrometry-based shotgun sequencing to examine the protein content of four major organellar compartments (cytosol, membranes [microsomes], mitochondria and nuclei) in six organs (brain, heart, kidney, liver, lung and placenta) of the laboratory mouse, Mus musculus. Using rigorous statistical filtering and machine-learning methods, the subcellular localization of 3274 of the 4768 proteins identified was determined with high-confidence, including 1503 previously uncharacterized factors, while tissue-selectivity was evaluated by comparison to previously reported mRNA expression patterns. This molecular compendium, fully accessible via a searchable web-browser interface, serves as a reliable reference of the expressed tissue and organelle proteomes of a leading model mammal. ... [Information of the supplier]
Organelle DB compiles protein localization data from organisms spanning the eukaryotic kingdom and presents an organized catalog of the known protein constituents of more than 50 organelles, subcellular structures, and protein complexes. The data sets in Organelle DB encompass 138 organisms with emphasis on the major model systems: S. cerevisiae, A. thaliana, D. melanogaster, C. elegans, M. musculus, and human proteins as well. In particular, Organelle DB is a central repository of yeast protein localization data, incorporating results from both previous and current (ongoing) large-scale studies of protein localization in Saccharomyces cerevisiae. In addition, we have manually curated several recent subcellular proteomic studies for incorporation in Organelle DB. In total, Organelle DB is a singular resource consolidating our knowledge of the protein composition of eukaryotic organelles and subcellular structures. ... [Information of the supplier]
PenBase provides comprehensive information about penaeidin properties, function, diversity and nomenclature. PenBase contains a Database section that lists all known penaeidins by subgroup or shrimp species. (...) Antimicrobial peptides are major components of innate immunity that have been conserved in evolution and found in different phyla of the plant and animal kingdom. Antimicrobial peptides are often small cationic molecules widely distributed in the whole living kingdom where they participate to host defence reactions against invading microorganisms. They are known to be involved in the innate immune response of vertebrate, invertebrate and plant species, and they are thought to be essential in organisms which lack adaptive immunity. Penaeidins are members of a family of antimicrobial peptides, originally isolated from the shrimp Litopenaeus vannamei, which present both Gram-positive antibacterial and antifungal activities (Destoumieux et al, 1997). Penaeidins appear to be a family of antimicrobial peptides ubiquitous among penaeid shrimps where they are major actors of the immune response (Bachère et al., 2004). ... [Information of the supplier]
PROSITE is a database of protein families and domains. It consists of biologically significant sites, patterns and profiles that help to reliably identify to which known protein family (if any) a new sequence belongs. [Information of the supplier]
MfunGD provides a resource for annotated mouse proteins and their occurence in protein networks. Protein function annotation is performed using the Functional Catalogue (FunCat) annotation scheme, which is a hierarchically structured classification system (Ruepp et al., NAR, 2004). To provide up-to-date similarity search results and InterPro domain analyses, the protein entries are interconnected with the SIMAP database (Rattei et al., NAR, 2006). The gene models are based on the RefSeq mouse cDNAs (Pruitt et al., NAR, 2007) The work of our group is focussed on the annotation of biological systems. Therefore, results from the Mammalian Protein-Protein Interaction Database ( MPPI, (Pagel et al., Bioinformatics, 2005 )) and the Comprehensive Resource of Mammalian Protein Complexes (CORUM, (Ruepp et al., NAR, 2007)) are linked to the MfunGD dataset. Links to external resources are also provided (e.g. Refseq, Uniprot, UCSC Genome Browser). MfunGD is implemented in GenRE, a J2EE based component oriented multi-tier architecture (Mewes et al., NAR, 2006). ... [Information of the supplier]
Peptidome is a public repository that archives and freely distributes tandem mass spectrometry peptide and protein identification data generated by the scientific community. Several layers of data are captured to promote understanding of the experiment and analysis of the underlying data. Peptidome was a public repository that archived tandem mass spectrometry peptide and protein identification data generated by the scientific community. This repository is now offline and is in archival mode. All data may be obtained from the Peptidome FTP site. ... [Information of the supplier]
Humans perceive numerous compounds as bitter. The bitterness of a compound often provides a hint to its potential toxicity, and aversion from bitterness helps refrain from consuming poisons. Well known example is strychnine. Some other bitter compounds, such as caffeine, while toxic in high dosages, are palatable and is consumed in large quantities. The amount of bitter compounds is estimated in thousands. But what are these compounds? How similar or different are their chemical properties? Do they act on the same or on different receptors? Is it possible to predict bitterness of a molecule? To enable investigation into these intriguing questions, we established BitterDB, a free and searchable database of bitter compounds. BitterDB currently holds over 550 bitter compounds obtained from the literature and from Merck index and their associated 25 human bitter taste receptors (hT2Rs). BitterDB provides several ways to investigate the bitter world: search for bitter compounds by different criteria, search for bitter molecules with structure similar to a query compound, blast bitter receptors and more. ... [Information of the supplier]
