The UCSD-Nature Signaling Gateway is a comprehensive and up-to-the-minute resource for anyone interested in signal transduction. This Gateway represents a unique collaboration between the University of California San Diego (UCSD) and Nature Publishing Group and is designed to facilitate navigation of the complex world of research into cellular signaling. Information and data presented here are freely available to all. It is powered by the San Diego Supercomputer Center (SDSC). At the heart of this collaboration is the Molecule Pages, a relational database of all significant published qualitative and quantitative information on cell signaling proteins. This database will also allow entirely new insights to be gleaned through intelligent data mining: the Molecule Pages database was developed with the specific aim of allowing interactions, and indeed whole pathways, to be modeled. Our goal is to filter the data to present only validated information. Thus, invited experts will enter much of the data and every Molecule Page will be comprehensively peer reviewed by Nature. We regard a Molecule Page as a new full-fledged form of publication. ... [Information of the supplier]
The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. A typical workflow includes the isolation and preparation of material for sequencing, a run of a sequencing machine in which sequencing data are produced and a subsequent bioinformatic analysis pipeline. ENA records this information in a data model that covers input information (sample, experimental setup, machine configuration), output machine data (sequence traces, reads and quality scores) and interpreted information (assembly, mapping, functional annotation). Data arrive at ENA from a variety of sources. These include submissions of raw data, assembled sequences and annotation from small-scale sequencing efforts, data provision from the major European sequencing centres and routine and comprehensive exchange with our partners in the International Nucleotide Sequence Database Collaboration (INSDC). ENA is made up of a number of distinct databases that includes EMBL-Bank, the newly established Sequence Read Archive (SRA) and the Trace Archive each with their own data formats and standards. ... [Information of the supplier]
The principal aims of the EGF are: a) to run the European School of Genetic Medicine, promoting the advanced scientific and professional training of young European Geneticists, with particular attention to the applications in the field of preventive medicine, b) to promote public education about genetics discoveries and c) to organize conferences, courses, international prizes and initiatives aimed at bringing together the scientific and humanistic disciplines. ... [Information of the supplier]
DNAtraffic database is dedicated to be an unique comprehensive and richly annotated database of genome dynamics during the cell life. DNAtraffic contains extensive data on the nomenclature, ontology, structure and function of proteins related to control of the DNA integrity mechanisms such as chromatin remodeling, DNA repair and damage response pathways from eight model organisms commonly used in the DNA-related study: Homo sapiens (human), Mus musculus (mouse), Drosophila melanogaster (fruit fly), Caenorhabditis elegans (nematode), Saccharomyces cerevisiae (budding yeast), Schizosaccharomyces pombe (fission yeast), Escherichia coli K-12, Arabidopsis thaliana (mouse-ear cress) DNAtraffic contains comprehensive information on diseases related to the assembled human proteins. Database is richly annotated in the systemic information on the nomenclature, chemistry and structure of the DNA damage and drugs targeting nucleic acids and/or proteins involved in the maintenance of genome stability. One of the DNAtraffic database aim is to create the first platform of the combinatorial complexity of DNA metabolism pathway analysis. Database includes illustrations of pathway, damage, protein and drug. Since DNAtraffic is designed to cover a broad spectrum of scientific disciplines it has to be extensively linked to numerous external data sources. Database represents the result of the manual annotation work aimed at making the DNAtraffic database much more useful for a wide range of systems biology applications. DNAtraffic database is freely available and can be queried by the name of DNA network process, DNA damage, protein, disease, and drug. ... [Information of the supplier]
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]