Proteomics databases
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[edit] Genomics databases - Quick Links
| STD Sequence Databases | DoTS | |
| ACeDB | GeneDB | |
| EPConDB | HuGeMap | |
| ORFanage | Virgil | |
| ZFIN | Genome Databases in Japan | |
| The Sanger Institute: AceDB Database |
[edit] Proteomics databases - Web Resources
Human protein reference database
A discovery resource for proteomics. The Human Protein Reference Database is a web-based resource based on open source technologies for protein information about several aspects of human proteins including protein–protein interactions, post-translational modifications, enzyme–substrate relationships and disease associations. This information was derived manually by a critical reading of the published literature by expert biologists and through bioinformatics analyses of the protein sequence. This database will assist in biomedical discoveries by serving as a resource of genomic and proteomic information and providing an integrated view of sequence, structure, function and protein networks in health and disease.
MitoProteome
Mitochondrial protein sequence database and annotation system. MitoProteome is an object-relational mitochondrial protein sequence database and annotation system. The initial release contains 847 human mitochondrial protein sequences, derived from public sequence databases and mass spectrometric analysis of highly purified human heart mitochondria. Each sequence is manually annotated with primary function, subfunction and subcellular location, and extensively annotated in an automated process with data extracted from external databases.
AAindex
AAindex is a database of amino acid indices and amino acid mutation matrices. An amino acid index is a set of 20 numerical values representing various physicochemical and biochemical properties of amino acids. An amino acid mutation matrix is generally a 20 x 20 numerical values representing similarity of amino acids. AAindex consists of two sections: AAindex1 for the collection of published amino acid indices and AAindex2 for the collection of published amino acid mutation matrices. Each entry of either AAindex1 or AAindex2 consists of the definition, the reference information, a list of related entries in terms of the correlation coefficient, and the actual data. The database may be accessed through the DBGET/LinkDB system at GenomeNet (http://www.genome.ad.jp/aaindex/) or may be downloaded by anonymous FTP (ftp://ftp.genome.ad.jp/pub/db/genomenet/aaindex/).
HIV Proteomics Resource
The HIV Proteomics Resource is a centralized database of HIV proteins and protein-specific bioinformatics tools. The HIV Proteomics Resource has 5 components: HIV proteome, HIV-1 cleavage sites, HIV protein datamining tool, HIV structure BLAST and proteomics tools directory. The HIV proteome section contains extensive data on each of the 19 HIV proteins, including functional characteristics, sample analyses of HIV-1 HXB2, structural models and links to other online resources. The cleavage sites section describes the position and sequence of Gag, Pol and Nef cleavage sites in relation to unique characteristics of subtype C viruses. The protein datamining tool allows for sequence analyses of 27 HIV-1 M-group isolates (subtype A through K), showing the influence of variation between subtypes. The HIV structure BLAST tool takes any amino acid sequence and lists similar HIV proteins with experimentally determined structures. The proteomics tools directory is a categorized list of websites and software relevant to HIV protein sequence/structure analysis.
YRC Public Data Repository (YRC PDR)
Provides advanced protein searching from multiple protein databases for many organisms. Provides protein annotations and raw experimental data from mass spectrometry, yeast two-hybrid, fluorescence microscopy, protein structure prediction and protein complex predictions for proteins from many organisms.
AARSDB
Aminoacyl-tRNA synthetase sequences.
Proteomics of Human Umbilical Vein Endothelial Cells (HUVECs)
The proteomic study of HUVEC using the classical approach combining two-dimensional electrophoresis (2-DE) and mass spectrometry (MALDI-TOF and LC-ESI-MS/MS) after peptide mass fingerprinting (PMF).
MitoP2
An integrated database on mitochondrial proteins in yeast and man. Comprehensive list of mitochondrial proteins of yeast and man. Based on the current literature we created an annotated reference set of yeast and human proteins. In addition, data sets relevant to the study of the mitochondrial proteome are integrated and accessible via search tools and links. They include computational predictions of signalling sequences, and summarize results from proteome mapping, mutant screening, expression profiling, protein–protein interaction and cellular sublocalization studies. For each individual approach, specificity and sensitivity for allocating mitochondrial proteins was calculated. By providing the evidence for mitochondrial candidate proteins the MitoP2 database lends itself to the genetic characterization of human mitochondriopathies.
3D-GENOMICS
Compares structural and functional annotations of proteins between sequenced genomes, annotations for the proteomes of many organisms using translated genomic sequences of the Prokaryota, Eukaryota and Archaea.
Database to compare structural and functional annotations of proteins between sequenced genomes. The 3D-GENOMICS database provides structural annotations for proteins from sequenced genomes. In August 2003 the database included data for 93 proteomes. The annotations stored in the database include homologous sequences from various sequence databases, domains from SCOP and Pfam, patterns from Prosite and other predicted sequence features such as transmembrane regions and coiled coils. In addition to annotations at the sequence level, several precomputed cross- proteome comparative analyses are available based on SCOP domain superfamily composition.
Rice Proteome Database
Administrated by National Institute of Agrobiological Sciences. It provides links to rice proteomics protocols, 2D-PAGE gels database, references and other useful links.
The Rice Proteome Database is the first detailed database to describe the proteome of rice. The current release contains 21 reference maps based on two-dimensional polyacrylamide gel electrophoresis (2D-PAGE) of proteins from rice tissues and subcellular compartments. These reference maps comprise 11 941 identified proteins showing tissue and subcellular localization, corresponding to 4180 separate protein entries in the database. The Rice Proteome Database contains the calculated properties of each protein such as molecular weight, isoelectric point and expression experimentally determined properties such as amino acid sequences obtained using protein sequencers and mass spectrometry and the results of database searches such as sequence homologies. The database is searchable by keyword, accession number, protein name, isoelectric point, molecular weight and amino acid sequence, or by selection of a spot on one of the 2D-PAGE reference maps. Cross-references are provided to tools for proteomics and to other 2D-PAGE databases, which in turn provide many links to other molecular databases.
OPD: Open Proteomics Database
Represented Organisms. Escherichia coli. .Homo sapiens. .Saccharomyces cerevisiae. .Mycobacterium smegmatis. .Mus musculus.. Links To Other Data. Unzip help. Introduction OPD is a public database for storing and disseminating mass ...
Integr8 - Access to complete genomes and proteomes
Integr8 - Access to complete genomes and proteomes Get for ?. .. Integr8. Home Proteomes and Genomes FASTA. About Integr8. History. Integr8 has been funded by the European Commission: from March 2006 - February 2009 under FELICS, contract ...
PENCE Proteome Analyst PA-GOSUB
This database has subcellular localization and GO general molecular function predictions for each protein with a very high coverage rate.
Home of the NESGC
A pilot project in structural genomics focused on proteins from eukaryotic model organisms and human. The project targets representative proteins to provide "coverage" of fold space, and those that are interesting from a functional genomics perspective.
2-DE Database for Human Heart Proteins
HEART-2DPAGE. The Human Myocardial Two-Dimensional Electrophoresis Protein Database. This is the two-dimensional polyacrylamide gel electrophoresis (2-D PAGE) database for human heart proteins. It contains data on proteins identified on ...
Proteome Database of Lactococcus lactis
DynaProt 2D: an advanced proteomic database for dynamic online access to proteomes and two-dimensional electrophoresis gels.
AGMLCentral-Home
AGML Central is a central location that includes tools for the creation of AGML (Annotated Gel Markup Language) XML document to analysis tools to analyse the 2-D Gel Electrophoretic data representeed in the AGML format.
BIOBASE Corporation
BIOBASE is a leading provider of manually curated biological databases and sophisticated analysis tools for the life science industry. BIOBASE’s product portfolio, referred as the BIOBASE Knowledge Library (BKL) includes industry standards such as TRANSFAC®, TRANSPATH®, YPD™ and HumanPSD™ databases. In combination BIOBASE’s powerful systems biology tool, ExPlain™, the BKL can be used to analyze complex regulatory networks and identify key molecules linked to human disease. In addition to the BKL, BIOBASE provides a growing collection of third-party databases including BRENDA® and Human Gene Mutation Database (HGMD®). More than 600 customers now license BIOBASE databases.
BIOBASE's Proteome databases contain comprehensive information about the entire proteomes of more than twenty species, from human, mouse, and rat (HumanPSD and GPCR-PD) to C. elegans (WormPD) to budding (YPD) and fission (PombePD) yeast, and human fungal pathogens (MycoPathPD). BIOBASE's powerful search tool, the Retriever, facilitates sophisticated searches and complex data analyses for all volumes of the Proteome databases. In addition, the BioKnowledge Workspace Viewer enables visualization of protein-protein interactions and interaction networks.
