The National Center for Biotechnology Information (NCBI) is part of the United States National Library of Medicine (NLM), a branch of the National Institutes of Health (NIH). It is approved and funded by the government of the United States. The NCBI is located in Bethesda, Maryland, and was founded in 1988 through legislation sponsored by US Congressman Claude Pepper.
Content-based image retrieval, also known as query by image content (QBIC) and content-based visual information retrieval (CBVIR), is the application of computer vision techniques to the image retrieval problem, that is, the problem of searching for digital images in large databases. Content-based image retrieval is opposed to traditional concept-based approaches.
The metabolome refers to the complete set of small-molecule chemicals found within a biological sample. The biological sample can be a cell, a cellular organelle, an organ, a tissue, a tissue extract, a biofluid or an entire organism. The small molecule chemicals found in a given metabolome may include both endogenous metabolites that are naturally produced by an organism as well as exogenous chemicals that are not naturally produced by an organism.
BRENDA is an information system representing one of the most comprehensive enzyme repositories. It is an electronic resource that comprises molecular and biochemical information on enzymes that have been classified by the IUBMB. Every classified enzyme is characterized with respect to its catalyzed biochemical reaction. Kinetic properties of the corresponding reactants are described in detail. BRENDA contains enzyme-specific data manually extracted from primary scientific literature and additional data derived from automatic information retrieval methods such as text mining. It provides a web-based user interface that allows a convenient and sophisticated access to the data.
The DrugBank database is a comprehensive, freely accessible, online database containing information on drugs and drug targets created and maintained by the University of Alberta and The Metabolomics Innovation Centre located in Alberta, Canada. As both a bioinformatics and a cheminformatics resource, DrugBank combines detailed drug data with comprehensive drug target information. DrugBank has used content from Wikipedia; Wikipedia also often links to Drugbank, posing potential circular reporting issues.
A receptor activated solely by a synthetic ligand (RASSL) or designer receptor exclusively activated by designer drugs (DREADD), is a class of artificially engineered protein receptors used in the field of chemogenetics which are selectively activated by certain ligands. They are used in biomedical research, in particular in neuroscience to manipulate the activity of neurons.
Virtual screening (VS) is a computational technique used in drug discovery to search libraries of small molecules in order to identify those structures which are most likely to bind to a drug target, typically a protein receptor or enzyme.
ChemSpider is a database of chemicals. ChemSpider is owned by the Royal Society of Chemistry.
BLAT is a pairwise sequence alignment algorithm that was developed by Jim Kent at the University of California Santa Cruz (UCSC) in the early 2000s to assist in the assembly and annotation of the human genome. It was designed primarily to decrease the time needed to align millions of mouse genomic reads and expressed sequence tags against the human genome sequence. The alignment tools of the time were not capable of performing these operations in a manner that would allow a regular update of the human genome assembly. Compared to pre-existing tools, BLAT was ~500 times faster with performing mRNA/DNA alignments and ~50 times faster with protein/protein alignments.
A taste receptor or tastant is a type of cellular receptor which facilitates the sensation of taste. When food or other substances enter the mouth, molecules interact with saliva and are bound to taste receptors in the oral cavity and other locations. Molecules which give a sensation of taste are considered "sapid".
Taste receptor 2 member 38 is a protein that in humans is encoded by the TAS2R38 gene. TAS2R38 is a bitter taste receptor; varying genotypes of TAS2R38 influence the ability to taste both 6-n-propylthiouracil (PROP) and phenylthiocarbamide (PTC). Though it has often been proposed that varying taste receptor genotypes could influence tasting ability, TAS2R38 is one of the few taste receptors shown to have this function.
Gustducin is a G protein associated with taste and the gustatory system, found in some taste receptor cells. Research on the discovery and isolation of gustducin is recent. It is known to play a large role in the transduction of bitter, sweet and umami stimuli. Its pathways are many and diverse.
Taste receptor type 2 member 1 (TAS2R1/T2R1) is a protein that in humans is encoded by the TAS2R1 gene. It belongs to the G protein-coupled receptor (GPCR) family and is related to class A-like GPCRs, they contain 7 transmembrane helix bundles and short N-terminus loop. Furthermore, TAS2R1 is member of the 25 known human bitter taste receptors, which enable the perception of bitter taste in the mouth cavity. Increasing evidence indicates a functional role of TAS2Rs in extra-oral tissues.
Taste receptor type 2 member 3 is a protein that in humans is encoded by the TAS2R3 gene.
Taste receptor type 2 member 4 is a protein that in humans is encoded by the TAS2R4 gene.
Taste receptors for bitter substances (T2Rs/TAS2Rs) belong to the family of G-protein coupled receptors and are related to class A-like GPCRs. There are 25 known T2Rs in humans responsible for bitter taste perception.
The gustatory system or sense of taste is the sensory system that is partially responsible for the perception of taste (flavor). Taste is the perception produced or stimulated when a substance in the mouth reacts chemically with taste receptor cells located on taste buds in the oral cavity, mostly on the tongue. Taste, along with olfaction and trigeminal nerve stimulation, determines flavors of food and other substances. Humans have taste receptors on taste buds and other areas, including the upper surface of the tongue and the epiglottis. The gustatory cortex is responsible for the perception of taste.
GeneCards is a database of human genes that provides genomic, proteomic, transcriptomic, genetic and functional information on all known and predicted human genes. It is being developed and maintained by the Crown Human Genome Center at the Weizmann Institute of Science, in collaboration with LifeMap Sciences.
The E. coli Metabolome Database (ECMDB) is a comprehensive, high-quality, freely accessible, online database of small molecule metabolites found in or produced by Escherichia coli. Escherichia coli is perhaps the best studied bacterium on earth and has served as the "model microbe" in microbiology research for more than 60 years. The ECMDB is essentially an E. coli "omics" encyclopedia containing detailed data on E. coli's genome, proteome and its metabolome. ECMDB is part of a suite of organism-specific metabolomics databases that includes DrugBank, HMDB, YMDB and SMPDB. As a metabolomics resource, the ECMDB is designed to facilitate research in the area gut/microbiome metabolomics and environmental metabolomics. The ECMDB contains two kinds of data: 1) chemical data and 2) molecular biology and/or biochemical data. The chemical data includes more than 2700 metabolite structures with detailed metabolite descriptions along with nearly 5000 NMR, GC-MS and LC-MS spectra corresponding to these metabolites. The biochemical data includes nearly 1600 protein sequences and more than 3100 biochemical reactions that are linked to these metabolite entries. Each metabolite entry in the ECMDB contains more than 80 data fields with approximately 65% of the information being devoted to chemical data and the other 35% of the information devoted to enzymatic or biochemical data. Many data fields are hyperlinked to other databases. The ECMDB also has a variety of structure and pathway viewing applets. The ECMDB database offers a number of text, sequence, spectral, chemical structure and relational query searches. These are described in more detail below.
The evolution of bitter taste receptors has been one of the most dynamic evolutionary adaptations to arise in multiple species. This phenomenon has been widely studied in the field of evolutionary biology because of its role in the identification of toxins often found on the leaves of inedible plants. A palate more sensitive to these bitter tastes would, theoretically, have an advantage over members of the population less sensitive to these poisonous substances because they would be much less likely to ingest toxic plants. Bitter-taste genes have been found in a variety of species, and the same genes have been well characterized in several common laboratory animals such as primates and mice, as well as in humans. The primary gene responsible for encoding this ability in humans is the TAS2R gene family which contains 25 functional loci as well as 11 pseudogenes. The development of this gene has been well characterized, with proof that the ability evolved before the human migration out of Africa. The gene continues to evolve in the present day.
