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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] |
Database
In computing, a database is an organized collection of data or a type of data store based on the use of a database management system (DBMS), the software that interacts with end users, applications, and the database itself to capture and analyze the data. The DBMS additionally encompasses the core facilities provided to administer the database. The sum total of the database, the DBMS and the associated applications can be referred to as a database system. Often the term "database" is also used loosely to refer to any of the DBMS, the database system or an application associated with the database. Before digital storage and retrieval of data have become widespread, index cards were used for data storage in a wide range of applications and environments: in the home to record and store recipes, shopping lists, contact information and other organizational data; in business to record presentation notes, project research and notes, and contact information; in schools as flash c ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Search Algorithm
In computer science, a search algorithm is an algorithm designed to solve a search problem. Search algorithms work to retrieve information stored within particular data structure, or calculated in the Feasible region, search space of a problem domain, with Continuous or discrete variable, either discrete or continuous values. Although Search engine (computing), search engines use search algorithms, they belong to the study of information retrieval, not algorithmics. The appropriate search algorithm to use often depends on the data structure being searched, and may also include prior knowledge about the data. Search algorithms can be made faster or more efficient by specially constructed database structures, such as search trees, hash maps, and database indexes. Search algorithms can be classified based on their mechanism of searching into three types of algorithms: linear, binary, and hashing. Linear search algorithms check every record for the one associated with a target key i ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Reaction Mechanism
In chemistry, a reaction mechanism is the step by step sequence of elementary reactions by which overall chemical reaction occurs. A chemical mechanism is a theoretical conjecture that tries to describe in detail what takes place at each stage of an overall chemical reaction. The detailed steps of a reaction are not observable in most cases. The conjectured mechanism is chosen because it is thermodynamically feasible and has experimental support in isolated intermediates (see next section) or other quantitative and qualitative characteristics of the reaction. It also describes each reactive intermediate, activated complex, and transition state, which bonds are broken (and in what order), and which bonds are formed (and in what order). A complete mechanism must also explain the reason for the reactants and catalyst used, the stereochemistry observed in reactants and products, all products formed and the amount of each. The electron or arrow pushing method is often used in ... [...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] |
Chemical Stability
In chemistry, chemical stability is the thermodynamic stability of a chemical system, in particular a chemical compound or a polymer. Colloquially, it may instead refer to kinetic persistence, the shelf-life of a metastable substance or system; that is, the timescale over which it begins to degrade. Thermodynamic stability occurs when a system is in its lowest energy state, or in chemical equilibrium with its environment. This may be a dynamic equilibrium in which individual atoms or molecules change form, but their overall number in a particular form is conserved. This type of chemical thermodynamic equilibrium will persist indefinitely unless the system is changed. Chemical systems might undergo changes in the phase of matter or a set of chemical reactions. State A is said to be more thermodynamically stable than state B if the Gibbs free energy of the change from A to B is positive. Versus reactivity Thermodynamic stability applies to a particular system. The reacti ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Mass Spectrometry
Mass spectrometry (MS) is an analytical technique that is used to measure the mass-to-charge ratio of ions. The results are presented as a ''mass spectrum'', a plot of intensity as a function of the mass-to-charge ratio. Mass spectrometry is used in many different fields and is applied to pure samples as well as complex mixtures. A mass spectrum is a type of plot of the ion signal as a function of the mass-to-charge ratio. These spectra are used to determine the elemental or isotopic signature of a sample, the masses of particles and of molecules, and to elucidate the chemical identity or structure of molecules and other chemical compounds. In a typical MS procedure, a sample, which may be solid, liquid, or gaseous, is ionization, ionized, for example by bombarding it with a Electron ionization, beam of electrons. This may cause some of the sample's molecules to break up into positively charged fragments or simply become positively charged without fragmenting. These ions (fragmen ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
NMR Spectra Database
A nuclear magnetic resonance spectra database is an electronic repository of information concerning Nuclear magnetic resonance (NMR) spectra. Such repositories can be downloaded as self-contained data sets or used online. The form in which the data is stored varies, ranging from line lists that can be graphically displayed to raw free induction decay (FID) data. Data is usually annotated in a way that correlates the spectral data with the related molecular structure. Data format Line list The form in which most NMR is described in literature papers. It is common for databases to display line lists graphically in a manner that is similar to how processed spectra might appear. These line list however lack first and higher order splitting, satellites from low abundance isotopes like carbon or platinum, as well as the information concerning line width and other informative aspects of line shape. The advantage of a line list is that it requires a minimal amount of memory. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cambridge Structural Database
The Cambridge Structural Database (CSD) is both a repository and a validated and curated resource for the three-dimensional structural data of molecules generally containing at least carbon and hydrogen, comprising a wide range of organic, metal-organic and organometallic molecules. The specific entries are complementary to the other crystallographic databases such as the Protein Data Bank (PDB), Inorganic Crystal Structure Database and International Centre for Diffraction Data. The data, typically obtained by X-ray crystallography and less frequently by electron diffraction or neutron diffraction, and submitted by crystallographers and chemists from around the world, are freely accessible (as deposited by authors) on the Internet via the CSD's parent organization's website (CCDC, Repository). The CSD is overseen by the not-for-profit incorporated company called the Cambridge Crystallographic Data Centre, CCDC. The CSD is a widely used repository for small-molecule organic ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Data Bank
The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules such as proteins and nucleic acids, which is overseen by the Worldwide Protein Data Bank (wwPDB). This structural data is obtained and deposited by biologists and biochemists worldwide through the use of experimental methodologies such as X-ray crystallography, Nuclear magnetic resonance spectroscopy of proteins, NMR spectroscopy, and, increasingly, cryo-electron microscopy. All submitted data are reviewed by expert Biocuration, biocurators and, once approved, are made freely available on the Internet under the CC0 Public Domain Dedication. Global access to the data is provided by the websites of the wwPDB member organizations (PDBe, PDBj, RCSB PDB, and BMRB). The PDB is a key in areas of structural biology, such as structural genomics. Most major scientific journals and some funding agencies now require scientists to submit their structure data to the PDB. Many other ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Crystallographic Databases
A crystallographic database is a database specifically designed to store information about the structure of molecules and crystals. Crystals are solids having, in all three dimensions of space, a regularly repeating arrangement of atoms, ions, or molecules. They are characterized by symmetry, morphology, and directionally dependent physical properties. A crystal structure describes the arrangement of atoms, ions, or molecules in a crystal. (Molecules need to crystallize into solids so that their regularly repeating arrangements can be taken advantage of in X-ray, neutron, and electron diffraction based crystallography). Crystal structures of crystalline material are typically determined from X-ray or neutron single-crystal diffraction data and stored in crystal structure databases. They are routinely identified by comparing reflection intensities and lattice spacings from X-ray powder diffraction data with entries in powder-diffraction fingerprinting databases. Crystal structure ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Chemical Abstracts Service
Chemical Abstracts Service (CAS) is a division of the American Chemical Society. It is a source of chemical information and is located in Columbus, Ohio, United States. Print periodicals ''Chemical Abstracts'' is a periodical index that provides numerous tools such as SciFinder as well as tagged keywords, summaries, indexes of disclosures, and structures of compounds in recently published scientific documents. Approximately 8,000 academic journal, journals, technical reports, dissertations, conference proceedings, and new books, available in at least 50 different languages, are monitored yearly, as are patent specifications from 27 countries and two international organizations. ''Chemical Abstracts'' ceased print publication on January 1, 2010. Databases The two principal databases that support the different products are CAplus and Registry. CAS References CAS References consists of bibliographic information and abstracts for all articles in chemical journals worldwide, and ch ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
