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]
PlasmoDB is a genome database for the genus Plasmodium, a set of single-celled eukaryotic pathogens that cause human and animal diseases, including malaria. [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]
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]
hiPathDB provides two different types of integration. The pathway-level integration is a simple collection of individual pathways as described in the original database. We devised a gene-centric pathway model that could reflect different properties of four databases. The entity-level integration creates a super pathway that merged all pathways by unifying redundant components. Even though the detailed molecular information such as complex formation or modification can be lost in some cases, the merged superpathway provides a unified view of current knowledge on human pathways, which is critical to understand relationships among different pathways. Another strong merit of hiPathDB is the built-in pathway visualization module to support explorative study of complex networks in an interactive fashion. The force-directed layout algorithm is optimized for almost automatic visualization of pathways. ... [Information of the supplier]
The Death domain (DD) superfamily is one of the largest classes of protein interaction modules and plays a pivotal role in the apoptosis, inflammation, necrosis, and immune cell signaling pathways. Critical caspase activating complexes in the apoptosis and inflammation signaling pathways are assembled via the DD superfamily. These domains are also involved in recruiting downstream effectors for immune cell receptor signaling, intracellular pathogen sensing, and response to DNA damage. To stimulate future researches among scientists who are interested in the DD superfamily mediated signaling pathway, we have developed the Death Domain Database, a manually curated database that aims to provide comprehensive information on PPIs of human DD superfamily. The current version of the Death Domain Database documents 175 PPI pairs among 99 DDS by curating 295 peer-reviewed publications. The Death Domain Database provides a detailed summary of PPI data, which fits into 3 categories: interaction, characterization, and functional role. Users can find in-depth information specified in the literature on relevant analytical methods, structural information. The Death Domain Database has a user-friendly interface with several helpful features, including a search engine, an interaction map, and a function for cross-referencing useful external databases. Our Death Domain Database will provide a valuable tool to assist in understanding and organizing the molecular interaction network of the DD superfamily. ... [Information of the supplier]
The DistiLD database aims to increase the usage of existing genome-wide association studies (GWAS) results by making it easy to query and visualize disease-associated SNPs and genes in their chromosomal context. The database performs three important tasks: 1. published GWAS are collected from several sources and linked to standardized, international disease codes ICD10 codes) 2. data from the International HapMap Project are analyzed to define linkage disequilibrium (LD) blocks onto which SNPs and genes are mapped 3. the web interface makes it easy to query and visualize disease-associated SNPs and genes within LD blocks. ... [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]
No other database than ESTHER holds all alpha/beta hydrolase fold proteins together: Interpro, Prosite, Pfam, have multiple entries for subsets of this structural superfamily. A table Synthese shows the correspondance between these database entries and the subfamilies in ESTHER. The ESTHER Table is now a little to big to be usefull. Each file contains one of the 31219 non redundant proteins/genes. The tables grouped in the family table, the syntheses table or the structure table may be more usefull. The Gene_locus nomenclature for these non-redundant entries is a name with 5 characters for the organisms (3 for genera, 2 for the species, except when a common 5 character name exists. ex: ratno is for Rattus norvegicus and human for man. This allows us to keep close to the Swiss-Prot nomenclature). The last characters define the protein, ex: human-acche represents human acetylcholinesterase. ... [Information of the supplier]
SUPERFAMILY is a database of structural and functional annotation for all proteins and genomes. The SUPERFAMILY annotation is based on a collection of hidden Markov models, which represent structural protein domains at the SCOP superfamily level. A superfamily groups together domains which have an evolutionary relationship. The annotation is produced by scanning protein sequences from over 2,414 completely sequenced genomes against the hidden Markov models. For each protein you can: a) Submit sequences for SCOP classification; b) View domain organisation, sequence alignments and protein sequence details For each genome you can: a) Examine superfamily assignments, phylogenetic trees, domain organisation lists and networks; b) Check for over- and under-represented superfamilies within a genome For each superfamily you can: a) Inspect SCOP classification, functional annotation, Gene Ontology annotation, InterPro abstract and genome assignments; b) Explore taxonomic distribution of a superfamily across the tree of life All annotation, models and the database dump are freely available for download to everyone. SUPERFAMILY is a member of the InterPro consortium of protein annotation databases, and has been integrated into the Ensembl eukaryotic genome project and The Arabidopsis Information Resource. To date, the SUPERFAMILY publications have been cited over 1,000 times. SUPERFAMILY has been used in structural, functional, evolutionary and phylogenetic research projects. ... [Information of the supplier]
