The p53 tumor suppressor gene was initially identified as being essential for the DNA damage checkpoint, but it was subsequently found to have a broader function after cellular stress, such as oncogene activation or hypoxia. The p53 protein functions as a tetrameric transcription factor found at very low levels in normal unstressed cells. After stress, different pathways lead to post-translational modification of the protein and its stabilization. p53 database contains 16,000+ entries corresponding to TP53 mutations found in tumors, normal skin, and noncancerous diseases such as rheumatoid arthritis. The database also includes germline mutations found in Li-Fraumeni syndrome (LFS) and LFS-like syndrome. ... [Information of the supplier, modified]
SWISS-2DPAGE is an annotated two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) and SDS-PAGE database established in 1993 and maintained collaboratively by the Biomedical Proteomics Reasearch Group (BPRG) of the Geneva University and the Proteome Informatics Group of the Swiss Institute of Bioinformatics (SIB). The SWISS-2DPAGE database assembles data on proteins identified on various 2-D PAGE and SDS-PAGE maps. Each SWISS-2DPAGE entry contains textual data on one protein, including mapping procedures, physiological and pathological information, experimental data (isoelectric point, molecular weight, amino acid composition, peptide masses) and bibliographical references. In addition to this textual data, SWISS-2DPAGE provides several 2-D PAGE and SDS-PAGE images showing the experimentally determined location of the protein, as well as a theoretical region computed from the sequence protein, indicating where the protein might be found in the gel. Cross-references are provided to Medline and other federated databases. ... [Information of the supplier]
AACompIdent is a tool which allows the identification of a protein from its amino acid composition. It searches the Swiss-Prot and / or TrEMBL databases for proteins, whose amino acid compositions are closest to the amino acid composition given. [Information of the supplier]
This page allows you to test an antibody sequence against the Kabat sequence database. Any unusual residues (occurring in < 1% of chains in the database) will be reported to you. This allows the identification of potential cloning artifacts and sequencing errors. The current Kabat database contains 6014 light chains and 7895 heavy chains. ... [Information of the supplier]
BioMagResBank (BMRB) is the publicly-accessible depository for NMR results from peptides, proteins, and nucleic acids recognized by the International Society of Magnetic Resonance and by the IUPAC-IUBMB-IUPAB Inter-Union Task Group on the Standardization of Data Bases of Protein and Nucleic Acid Structures Determined by NMR Spectroscopy. In addition, BMRB provides reference information and maintains a collection of NMR pulse sequences and computer software for biomolecular NMR. Access to data in BMRB is free directly from its web site (URL http://www.bmrb.wisc.edu) and ftp site (ftp.bmrb.wisc.edu) and will remain so as public funding permits. The concept of a biomolecular NMR data bank was developed under a five-year research grant awarded to the University of Wisconsin-Madison from the National Library of Medicine, National Institutes of Health. ... [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]
