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Found 43 result(s)
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Starting September 2013, MINT uses the IntAct database infrastructure to limit the duplication of efforts and to optimise future software development. Data manually curated by the MINT curators can now be accessed from the IntAct homepage at the EBI. Data maintenance and release, MINT PSICQUIC and IMEx services are under the responsibility of the IntAct team, while curation effort will be carried by both groups. The MINT development team now focuses on two new developments: mentha that integrates protein interaction information curated by IMEx databases and SIGNOR a database of logic relationships between human proteins. MINT is a public repository for molecular interactions reported in peer-reviewed journals.IT is a collection of molecular interaction databases that can be used to search for, analyze and graphically display molecular interaction networks and pathways from a wide variety of species. MINT is comprised of separate database components. HomoMINT, is an inferred human protein interatction database. Domino, is database of domain peptide interactions. A new component has been added called VirusMINT that explores the interactions of viral proteins with human proteins.
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APID Interactomes (Agile Protein Interactomes DataServer) provides information on the protein interactomes of numerous organisms, based on the integration of known experimentally validated protein-protein physical interactions (PPIs). The interactome data includes a report on quality levels and coverage over the proteomes for each organism included. APID integrates PPIs from primary databases of molecular interactions (BIND, BioGRID, DIP, HPRD, IntAct, MINT) and also from experimentally resolved 3D structures (PDB) where more than two distinct proteins have been identified. This collection references protein interactors, through a UniProt identifier.
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IntAct provides a freely available, open source database system and analysis tools for molecular interaction data. All interactions are derived from literature curation or direct user submissions and are freely available.
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<<<!!!<<<migrated to Integrated Interactions Database r3d100012380>>>!!!>>>
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HPIDB is a public resource, which integrates experimental PPIs from various databases into a single database. The Host-Pathogen Interaction Database (HPIDB) is a genomics resource devoted to understanding molecular interactions between key organisms and the pathogens to which they are susceptible.
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InnateDB is a publicly available database of the genes, proteins, experimentally-verified interactions and signaling pathways involved in the innate immune response of humans, mice and bovines to microbial infection. The database captures an improved coverage of the innate immunity interactome by integrating known interactions and pathways from major public databases together with manually-curated data into a centralised resource. The database can be mined as a knowledgebase or used with our integrated bioinformatics and visualization tools for the systems level analysis of the innate immune response.
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<<<!!!<<< This repository is no longer available. 2019-02-19 >>>!!!>>>
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The European Bioinformatics Institute (EBI) has a long-standing mission to collect, organise and make available databases for biomolecular science. It makes available a collection of databases along with tools to search, download and analyse their content. These databases include DNA and protein sequences and structures, genome annotation, gene expression information, molecular interactions and pathways. Connected to these are linking and descriptive data resources such as protein motifs, ontologies and many others. In many of these efforts, the EBI is a European node in global data-sharing agreements involving, for example, the USA and Japan.
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MatrixDB is a freely available database focused on interactions established by extracellular proteins and polysaccharides. MatrixDB takes into account the multimetric nature of the extracellular proteins (e.g. collagens, laminins and thrombospondins are multimers). MatrixDB includes interaction data extracted from the literature by manual curation in our lab, and offers access to relevant data involving extracellular proteins provided by our IMEx partner databases through the PSICQUIC webservice, as well as data from the Human Protein Reference Database. MatrixDB is in charge of the curation of papers published in Matrix Biology since January 2009
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The Toxin and Toxin Target Database is a unique bioinformatics resource that combines detailed toxin data with comprehensive toxin target information. The focus of the T3DB is on providing mechanisms of toxicity and target proteins for each toxin. This dual nature of the T3DB, in which toxin and toxin target records are interactively linked in both directions, makes it unique from existing databases.
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STRING is a database of known and predicted protein interactions. The interactions include direct (physical) and indirect (functional) associations; they are derived from four sources: - Genomic Context - High-throughput Experiments - (Conserved) Coexpression - Previous Knowledge STRING quantitatively integrates interaction data from these sources for a large number of organisms, and transfers information between these organisms where applicable.
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The Biological General Repository for Interaction Datasets (BioGRID) is a public database that archives and disseminates genetic and protein interaction data from model organisms and humans. BioGRID is an online interaction repository with data compiled through comprehensive curation efforts. All interaction data are freely provided through our search index and available via download in a wide variety of standardized formats.
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The Database explores the interactions of chemicals and proteins. It integrates information about interactions from metabolic pathways, crystal structures, binding experiments and drug-target relationships. Inferred information from phenotypic effects, text mining and chemical structure similarity is used to predict relations between chemicals. STITCH further allows exploring the network of chemical relations, also in the context of associated binding proteins.
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mentha archives evidence collected from different sources and presents these data in a complete and comprehensive way. Its data comes from manually curated protein-protein interaction databases that have adhered to the IMEx consortium. The aggregated data forms an interactome which includes many organisms. mentha is a resource that offers a series of tools to analyse selected proteins in the context of a network of interactions. Protein interaction databases archive protein-protein interaction (PPI) information from published articles. However, no database alone has sufficient literature coverage to offer a complete resource to investigate "the interactome". mentha's approach generates every week a consistent interactome (graph). Most importantly, the procedure assigns to each interaction a reliability score that takes into account all the supporting evidence. mentha offers eight interactomes (Homo sapiens, Arabidopsis thaliana, Caenorhabditis elegans, Drosophila melanogaster, Escherichia coli K12, Mus musculus, Rattus norvegicus, Saccharomyces cerevisiae) plus a global network that comprises every organism, including those not mentioned. The website and the graphical application are designed to make the data stored in mentha accessible and analysable to all users. Source databases are: MINT, IntAct, DIP, MatrixDB and BioGRID.
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ConsensusPathDB integrates interaction networks in humans (and in the model organisms - yeast and mouse) including binary and complex protein-protein, genetic, metabolic, signaling, gene regulatory and drug-target interactions, as well as biochemical pathways. Data originate from public resources for interactions and interactions curated from the literature. The interaction data are integrated in a complementary manner to avoid redundancies.
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The IMEx consortium is an international collaboration between a group of major public interaction data providers who have agreed to share curation effort and develop and work to a single set of curation rules when capturing data from both directly deposited interaction data or from publications in peer-reviewed journals, capture full details of an interaction in a “deep” curation model, perform a complete curation of all protein-protein interactions experimentally demonstrated within a publication, make these interaction available in a single search interface on a common website, provide the data in standards compliant download formats, make all IMEx records freely accessible under the Creative Commons Attribution License
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<<<!!!<<< This repository is no longer available. >>>!!!>>>
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<<<!!!<<< as stated 2017-06-09 MPIDB is no longer available under URL http://www.jcvi.org/mpidb/about.php >>>!!!>>> The microbial protein interaction database (MPIDB) aims to collect and provide all known physical microbial interactions. Currently, 24,295 experimentally determined interactions among proteins of 250 bacterial species/strains can be browsed and downloaded. These microbial interactions have been manually curated from the literature or imported from other databases (IntAct, DIP, BIND, MINT) and are linked to 26,578 experimental evidences (PubMed ID, PSI-MI methods). In contrast to these databases, interactions in MPIDB are further supported by 68,346 additional evidences based on interaction conservation, protein complex membership, and 3D domain contacts (iPfam, 3did). We do not include (spoke/matrix) binary interactions infered from pull-down experiments.
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virus mentha archives evidence about viral interactions collected from different sources and presents these data in a complete and comprehensive way. Its data comes from manually curated protein-protein interaction databases that have adhered to the IMEx consortium. virus mentha is a resource that offers a series of tools to analyse selected proteins in the context of a network of interactions. Protein interaction databases archive protein-protein interaction (PPI) information from published articles. However, no database alone has sufficient literature coverage to offer a complete resource to investigate "the interactome". virus mentha's approach generates every week a consistent interactome (graph). Most importantly, the procedure assigns to each interaction a reliability score that takes into account all the supporting evidence. virus mentha offers direct access to viral families such as: Orthomyxoviridae, Orthoretrovirinae and Herpesviridae plus, it offers the unique possibility of searching by host organism. The website and the graphical application are designed to make the data stored in virus mentha accessible and analysable to all users.virus mentha superseeds VirusMINT. The Source databases are: MINT, DIP, IntAct, MatrixDB, BioGRID.
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The DIP database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. The data stored within the DIP database were curated, both, manually by expert curators and also automatically using computational approaches that utilize the the knowledge about the protein-protein interaction networks extracted from the most reliable, core subset of the DIP data. Please, check the reference page to find articles describing the DIP database in greater detail. The Database of Ligand-Receptor Partners (DLRP) is a subset of DIP (Database of Interacting Proteins). The DLRP is a database of protein ligand and protein receptor pairs that are known to interact with each other. By interact we mean that the ligand and receptor are members of a ligand-receptor complex and, unless otherwise noted, transduce a signal. In some instances the ligand and/or receptor may form a heterocomplex with other ligands/receptors in order to be functional. We have entered the majority of interactions in DLRP as full DIP entries, with links to references and additional information
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Primate Cell Type Database, a publicly available web-accessible archive of intracellular patch clamp recordings and highly detailed three-dimensional digital reconstructions of neuronal morphology.
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Numerical database of atomic and molecular processes and particle-surface interactions. ALADDIN has formatted data on atomic structure and spectra (energy levels,wave lengths, and transition probabilities); electron and heavy particle collisions with atoms, ions, and molecules (cross sections and/or rate coefficients, including, in most cases, analytic fit to the data); sputtering of surfaces by impact of main plasma constituents and self sputtering; particle reflection from surfaces; thermophysical and thermomechanical properties of beryllium and pyrolytic graphites.
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The Yeast Resource Center provides access to data about mass spectrometry, yeast two-hybrid arrays, deconvolution florescence microscopy, protein structure prediction and computational biology. These services are provided to further the goal of a complete understanding of the chemical interactions required for the maintenance and faithful reproduction of a living cell. The observation that the fundamental biological processes of yeast are conserved among all eukaryotes ensures that this knowledge will shape and advance our understanding of living systems.
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RADAM portal is an interface to the network of RADAM (RADiation DAMage) Databases collecting data on interactions of ions, electrons, positrons and photons with biomolecular systems, on radiobiological effects and relevant phenomena occurring at different time, spatial and energy scales in irradiated targets during and after the irradiation. This networking system has been created by the Consortium of COST Action MP1002 (Nano-IBCT: Nano-scale insights into Ion Beam Cancer Therapy) during 2011-2014 using the Virtual Atomic and Molecular Data Center (VAMDC) standards.