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ZINC Database
The ZINC database (recursive acronym: ''ZINC is not commercial'') is a curated collection of commercially available chemical compounds prepared especially for virtual screening. ZINC is used by investigators (generally people with training as biologists or chemists) in pharmaceutical companies, biotechnology companies, and research universities. Scope and access ZINC is different from other chemical databases because it aims to represent the biologically relevant, three dimensional form of the molecule. Curation and updates ZINC is updated regularly and may be downloaded and used free of charge. It is developed by John Irwin in the Shoichet Laboratory in the Department of Pharmaceutical Chemistry at the University of California, San Francisco. Version The latest release of the website interface is "ZINC-22". The database is continuously updated and is claimed to contain over 37 billion commercially available molecules. Uses The database is typically used for molecule ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Zinc Logo
Zinc is a chemical element; it has symbol Zn and atomic number 30. It is a slightly brittle metal at room temperature and has a shiny-greyish appearance when oxidation is removed. It is the first element in group 12 (IIB) of the periodic table. In some respects, zinc is chemically similar to magnesium: both elements exhibit only one normal oxidation state (+2), and the Zn2+ and Mg2+ ions are of similar size. Zinc is the 24th most abundant element in Earth's crust and has five stable isotopes. The most common zinc ore is sphalerite (zinc blende), a zinc sulfide mineral. The largest workable lodes are in Australia, Asia, and the United States. Zinc is refined by froth flotation of the ore, roasting, and final extraction using electricity (electrowinning). Zinc is an essential trace element for humans, animals, plants and for microorganisms and is necessary for prenatal and postnatal development. It is the second most abundant trace metal in humans after iron, an important cof ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecule
A molecule is a group of two or more atoms that are held together by Force, attractive forces known as chemical bonds; depending on context, the term may or may not include ions that satisfy this criterion. In quantum physics, organic chemistry, and biochemistry, the distinction from ions is dropped and ''molecule'' is often used when referring to polyatomic ions. A molecule may be homonuclear, that is, it consists of atoms of one chemical element, e.g. two atoms in the oxygen molecule (O2); or it may be heteronuclear, a chemical compound composed of more than one element, e.g. water (molecule), water (two hydrogen atoms and one oxygen atom; H2O). In the kinetic theory of gases, the term ''molecule'' is often used for any gaseous particle regardless of its composition. This relaxes the requirement that a molecule contains two or more atoms, since the noble gases are individual atoms. Atoms and complexes connected by non-covalent interactions, such as hydrogen bonds or ionic ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ultra-large-scale Docking
Ultra-large-scale docking, sometimes abbreviated as Ultra-LSD, is an ultra-large-scale approach to protein–ligand docking and virtual screening. It employs molecular docking campaigns against libraries of millions or billions of chemical compounds to discover new drugs. The virtual screening phase identifies potential high-affinity ligands and then selected promising compounds are synthesized and further evaluated in the laboratory, including in terms of properties like functional activity and selectivity. The purpose of Ultra-LSD is to discover novel chemical scaffolds for ligands of molecular targets. Ultra-LSD was developed by Brian Shoichet and John Irwin at the University of California, San Francisco, Bryan L. Roth at University of North Carolina at Chapel Hill, and other colleagues, and was first described in 2019. The researchers have conducted Ultra-LSD campaigns against a variety of targets, including the serotonin 5-HT2A receptor, the melatonin receptors, the dopami ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
ChEMBL
ChEMBL or ChEMBLdb is a manually curated chemical database of bioactive molecules with drug inducing properties. It is maintained by the European Bioinformatics Institute (EBI), of the European Molecular Biology Laboratory ( EMBL), based at the Wellcome Trust Genome Campus, Hinxton, UK. The database, originally known as StARlite, was developed by a biotechnology company called Inpharmatica Ltd. later acquired by Galapagos NV. The data was acquired for EMBL in 2008 with an award from The Wellcome Trust, resulting in the creation of the ChEMBL chemogenomics group at EMBL-EBI, led by John Overington. Scope and access The ChEMBL database contains compound bioactivity data against drug targets. Bioactivity is reported in Ki, Kd, IC50, and EC50. Data can be filtered and analyzed to develop compound screening libraries for lead identification during drug discovery. ChEMBL version 2 (ChEMBL_02) was launched in January 2010, including 2.4 million bioassay measurements covering 622, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
National Center For Biotechnology Information
The National Center for Biotechnology Information (NCBI) is part of the 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. The NCBI houses a series of databases relevant to biotechnology and biomedicine and is an important resource for bioinformatics tools and services. Major databases include GenBank for DNA sequences and PubMed, a bibliographic database for biomedical literature. Other databases include the NCBI Epigenomics database. All these databases are available online through the Entrez search engine. NCBI was directed by David Lipman, one of the original authors of the BLAST sequence alignment program and a widely respected figure in bioinformatics. GenBank NCBI had responsibility for making available the GenBank DNA seque ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
PubChem
PubChem is a database of Chemistry, chemical molecules and their activities against biological assays. The system is maintained by the National Center for Biotechnology Information (NCBI), a component of the National Library of Medicine, which is part of the United States National Institutes of Health (NIH). PubChem can be accessed for free through a web user interface. Millions of compound structures and descriptive datasets can be freely downloaded via FTP. PubChem contains multiple substance descriptions and small molecules with fewer than 100 atoms and 1,000 bonds. More than 80 database vendors contribute to the growing PubChem database. History PubChem was released in 2004 as a component of the Molecular Libraries Program (MLP) of the NIH. As of November 2015, PubChem contains more than 150 million depositor-provided substance descriptions, 60 million unique chemical structures, and 225 million biological activity test results (from over 1 million assay experiments performe ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
High-throughput Screening
High-throughput screening (HTS) is a method for scientific discovery especially used in drug discovery and relevant to the fields of biology, materials science and chemistry. Using robotics, data processing/control software, liquid handling devices, and sensitive detectors, high-throughput screening allows a researcher to quickly conduct millions of chemical, genetic, or pharmacological tests. Through this process one can quickly recognize active compounds, antibodies, or genes that modulate a particular biomolecular pathway. The results of these experiments provide starting points for drug design and for understanding the noninteraction or role of a particular location. Assay plate preparation The key labware or testing vessel of HTS is the microtiter plate, which is a small container, usually disposable and made of plastic, that features a grid of small, open divots called ''wells''. In general, microplates for HTS have either 96, 192, 384, 1536, 3456 or 6144 wells. These are a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Quantitative Structure–activity Relationship
Quantitative structure–activity relationship models (QSAR models) are regression or classification models used in the chemical and biological sciences and engineering. Like other regression models, QSAR regression models relate a set of "predictor" variables (X) to the potency of the response variable (Y), while classification QSAR models relate the predictor variables to a categorical value of the response variable. In QSAR modeling, the predictors consist of physico-chemical properties or theoretical molecular descriptors of chemicals; the QSAR response-variable could be a biological activity of the chemicals. QSAR models first summarize a supposed relationship between chemical structures and biological activity in a data-set of chemicals. Second, QSAR models predict the activities of new chemicals. Related terms include ''quantitative structure–property relationships'' (''QSPR'') when a chemical property is modeled as the response variable. "Different properties or ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecule Mining
Molecule mining is the process of data mining, or extracting and discovering patterns, as applied to molecules. Since molecules may be represented by molecular graphs, this is strongly related to graph mining and structured data mining. The main problem is how to represent molecules while discriminating the data instances. One way to do this is chemical similarity metrics, which has a long tradition in the field of cheminformatics. Typical approaches to calculate chemical similarities use chemical fingerprints, but this loses the underlying information about the molecule topology. Mining the molecular graphs directly avoids this problem. So does the inverse QSAR problem which is preferable for vectorial mappings. Coding(Moleculei,Moleculej≠i) Kernel methods * Marginalized graph kernelH. Kashima, K. Tsuda, A. Inokuchi, Marginalized Kernels Between Labeled Graphs, The 20th International Conference on Machine Learning (ICML2003), 2003. PDF * Optimal assignment kernelH. F ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
University Of California, San Francisco
The University of California, San Francisco (UCSF) is a Public university, public Land-grant university, land-grant research university in San Francisco, California, United States. It is part of the University of California system and is dedicated entirely to health science and life science. It conducts research and teaching in Medicine, medical and biology, biological sciences. UCSF was founded as Toland Medical College in 1864. In 1873, it became affiliated with the University of California as its Medical Department. In the same year, it incorporated the California College of Pharmacy and in 1881 it established a dentistry school. Its facilities were located in both Berkeley, California, Berkeley and San Francisco. In 1964, the school gained full administrative independence as a campus of the UC system, headed by its own chancellor, and in 1970 it gained its current name. Historically based at List of neighborhoods in San Francisco#Parnassus, Parnassus Heights with satellite ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Free As In Beer
The adjective ''free'' in English is commonly used in one of two meanings: "at no monetary cost" (''gratis'') or "with little or no restriction" (''libre''). This ambiguity can cause issues where the distinction is important, as it often is in dealing with laws concerning the use of information, such as copyright and patents. The terms ''gratis'' and ''libre'' may be used to categorise intellectual property like computer programs, according to the licenses and legal restrictions that cover them, especially in the free software and open source communities, as well as the broader free culture movement. For example, they are used to distinguish "freeware" (software ''gratis'') from free software (software ''libre''). Free software advocate and GNU founder Richard Stallman advocates usage of the slogan: "Think free as in free speech, not free beer." This basically means: "Think free as in ''libre'', not ''gratis''." ''Gratis'' ''Gratis'' () in English is adopted from the various ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Chemical Databases
A chemical database is a database specifically designed to store chemical information. This information is about chemical and crystal structures, spectra, reactions and syntheses, and thermophysical data. Types of chemical databases Bioactivity database Bioactivity databases correlate structures or other chemical information to bioactivity results taken from bioassays in literature, patents, and screening programs. Chemical structures Chemical structures are traditionally represented using lines indicating chemical bonds between atoms and drawn on paper (2D structural formulae). While these are ideal visual representations for the chemist, they are unsuitable for computational use and especially for search and storage. Small molecules (also called ligands in drug design applications), are usually represented using lists of atoms and their connections. Large molecules such as proteins are however more compactly represented using the sequences of their amino acid buil ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
