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Chemical File Format
A chemical file format is a type of data file which is used specifically for depicting molecular data. One of the most widely used is the chemical table file format, which is similar to ''Structure Data Format'' (SDF) files. They are text files that represent multiple chemical structure records and associated data fields. The XYZ file format is a simple format that usually gives the number of atoms in the first line, a comment on the second, followed by a number of lines with atomic symbols (or atomic numbers) and cartesian coordinates. The Protein Data Bank Format is commonly used for proteins but is also used for other types of molecules. There are many other types which are detailed below. Various software systems are available to convert from one format to another. Distinguishing formats Chemical information is usually provided as files or streams and many formats have been created, with varying degrees of documentation. The format is indicated in three ways:(see ) * ''f ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Chemical Table File
Chemical table file (CT file) is a family of text-based chemical file formats that describe molecules and chemical reactions. One format, for example, lists each atom in a molecule, the x-y-z coordinates of that atom, and the bonds among the atoms. File formats There are several file formats in the family. The formats ''were'' created by MDL Information Systems (MDL), which was acquired by Symyx Technologies then merged with Accelrys Corp., and now called BIOVIA, a subsidiary of Dassault Systemes of Dassault Group. The CT file is an open format. BIOVIA publishes its specification. BIOVIA requires users to register to download the CT file format specifications. Molfile An MDL Molfile is a file format for holding information about the atoms, bonds, connectivity and coordinates of a molecule. The molfile consists of some header information, the Connection Table (CT) containing atom info, then bond connections and types, followed by sections for more complex information. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Structure
Protein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers specifically polypeptides formed from sequences of amino acids, which are the monomers of the polymer. A single amino acid monomer may also be called a ''residue'', which indicates a repeating unit of a polymer. Proteins form by amino acids undergoing condensation reactions, in which the amino acids lose one water molecule per reaction in order to attach to one another with a peptide bond. By convention, a chain under 30 amino acids is often identified as a peptide, rather than a protein. To be able to perform their biological function, proteins fold into one or more specific spatial conformations driven by a number of non-covalent interactions, such as hydrogen bonding, ionic interactions, Van der Waals forces, and hydrophobic packing. To understand the functions of proteins at a molecular level, it is often necessary to determine their three-dimensiona ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
OpenBabel
Open Babel is a free chemical informatics software designed to facilitate the conversion of Chemical file formats and manage molecular data. It serves as a chemical expert system, widely used in fields such as cheminformatics, molecular modelling, and computational chemistry. Open Babel provides both a comprehensive library and command-line utilities, making it a versatile tool for researchers, developers, and professionals. About Due to the strong relationship to informatics this program belongs more to the category cheminformatics than to molecular modelling. It is available for Windows, Unix, Linux, macOS, and Android. It is free and open-source software released under a GNU General Public License (GPL) 2.0. The project's stated goal is: "Open Babel is a community-driven scientific project assisting both users and developers as a cross-platform program and library designed to support molecular modeling, chemistry, and many related areas, including interconversion of file fo ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ethylene
Ethylene (IUPAC name: ethene) is a hydrocarbon which has the formula or . It is a colourless, flammable gas with a faint "sweet and musky" odour when pure. It is the simplest alkene (a hydrocarbon with carbon–carbon bond, carbon–carbon double bonds). Ethylene is widely used in the chemical industry, and its worldwide production (over 150 million tonnes in 2016) exceeds that of any other organic compound. Much of this production goes toward creating polyethylene, which is a widely used plastic containing polymer chains of ethylene units in various chain lengths. Production greenhouse gas emissions, emits greenhouse gases, including methane from feedstock production and carbon dioxide from any non-sustainable energy used. Ethylene is also an important natural plant hormone and is used in agriculture to induce ripening of fruits. The hydrate of ethylene is ethanol. Structure and properties This hydrocarbon has four hydrogen atoms bound to a pair of carbon atoms that are con ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ethanol
Ethanol (also called ethyl alcohol, grain alcohol, drinking alcohol, or simply alcohol) is an organic compound with the chemical formula . It is an Alcohol (chemistry), alcohol, with its formula also written as , or EtOH, where Et is the pseudoelement symbol for ethyl group, ethyl. Ethanol is a Volatility (chemistry), volatile, flammable, colorless liquid with a characteristic wine-like odor and pungent taste. As a psychoactive depressant, it is the active ingredient in alcoholic beverages, and the second most consumed drug globally behind caffeine. Ethanol is naturally produced by the fermentation process of sugars by yeasts or via petrochemical processes such as ethylene hydration. Historically it was used as a general anesthetic, and has modern medical applications as an antiseptic, disinfectant, solvent for some medications, and antidote for methanol poisoning and ethylene glycol poisoning. It is used as a chemical solvent and in the Chemical synthesis, synthesis of orga ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Methane
Methane ( , ) is a chemical compound with the chemical formula (one carbon atom bonded to four hydrogen atoms). It is a group-14 hydride, the simplest alkane, and the main constituent of natural gas. The abundance of methane on Earth makes it an economically attractive fuel, although capturing and storing it is difficult because it is a gas at standard temperature and pressure. In the Earth's atmosphere methane is transparent to visible light but absorbs infrared radiation, acting as a greenhouse gas. Methane is an Organic chemistry, organic Organic compound, compound, and among the simplest of organic compounds. Methane is also a hydrocarbon. Naturally occurring methane is found both below ground and under the seafloor and is formed by both geological and biological processes. The largest reservoir of methane is under the seafloor in the form of methane clathrates. When methane reaches the surface and the Atmosphere of Earth, atmosphere, it is known as atmospheric methane. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Hydrogen Atoms
A hydrogen atom is an atom of the chemical element hydrogen. The electrically neutral hydrogen atom contains a single positively charged proton in the nucleus, and a single negatively charged electron bound to the nucleus by the Coulomb force. Atomic hydrogen constitutes about 75% of the baryonic mass of the universe. In everyday life on Earth, isolated hydrogen atoms (called "atomic hydrogen") are extremely rare. Instead, a hydrogen atom tends to combine with other atoms in compounds, or with another hydrogen atom to form ordinary (diatomic) hydrogen gas, H2. "Atomic hydrogen" and "hydrogen atom" in ordinary English use have overlapping, yet distinct, meanings. For example, a water molecule contains two hydrogen atoms, but does not contain atomic hydrogen (which would refer to isolated hydrogen atoms). Atomic spectroscopy shows that there is a discrete infinite set of states in which a hydrogen (or any) atom can exist, contrary to the predictions of classical physics. Attem ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Simplified Molecular Input Line Entry System
The Simplified Molecular Input Line Entry System (SMILES) is a specification in the form of a line notation for describing the structure of chemical species using short ASCII strings. SMILES strings can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensional models of the molecules. The original SMILES specification was initiated in the 1980s. It has since been modified and extended. In 2007, an open standard called OpenSMILES was developed in the open source chemistry community. History The original SMILES specification was initiated by David Weininger at the USEPA Mid-Continent Ecology Division Laboratory in Duluth in the 1980s. Acknowledged for their parts in the early development were "Gilman Veith and Rose Russo (USEPA) and Albert Leo and Corwin Hansch (Pomona College) for supporting the work, and Arthur Weininger (Pomona; Daylight CIS) and Jeremy Scofield (Cedar River Software, Renton, WA) for assistance in programm ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Alanine
Alanine (symbol Ala or A), or α-alanine, is an α-amino acid that is used in the biosynthesis of proteins. It contains an amine group and a carboxylic acid group, both attached to the central carbon atom which also carries a methyl group side chain. Consequently it is classified as a non-polar, aliphatic α-amino acid. Under biological conditions, it exists in its zwitterionic form with its amine group protonated (as ) and its carboxyl group deprotonated (as ). It is non-essential to humans as it can be synthesized metabolically and does not need to be present in the diet. It is encoded by all codons starting with G C (GC U, GCC, GC A, and GCG). The L-isomer of alanine (left-handed) is the one that is incorporated into proteins. L-alanine is second only to L-leucine in rate of occurrence, accounting for 7.8% of the primary structure in a sample of 1,150 proteins. The right-handed form, D-alanine, occurs in peptides in some bacterial cell walls (in peptidoglycan) ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Benzene
Benzene is an Organic compound, organic chemical compound with the Chemical formula#Molecular formula, molecular formula C6H6. The benzene molecule is composed of six carbon atoms joined in a planar hexagonal Ring (chemistry), ring with one hydrogen atom attached to each. Because it contains only carbon and hydrogen atoms, benzene is classed as a hydrocarbon. Benzene is a natural constituent of petroleum and is one of the elementary petrochemicals. Due to the cyclic continuous pi bonds between the carbon atoms, benzene is classed as an aromatic hydrocarbon. Benzene is a colorless and highly Combustibility and flammability, flammable liquid with a sweet smell, and is partially responsible for the aroma of gasoline. It is used primarily as a Precursor (chemistry), precursor to the manufacture of chemicals with more complex structures, such as ethylbenzene and cumene, of which billions of kilograms are produced annually. Although benzene is a major Chemical industry, industrial che ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Markush Structure
A Markush structure, Markush group, or a Markush claim is a representation of alternatively useable members. Markush structures are frequently used with chemical structures to indicate a group of related chemical compounds. They are commonly used in chemistry texts and in List of patent claim types#Markush, patent claims. Markush structures are depicted with multiple independently variable groups, such as Side chain, R groups in which a side chain can have varying structure. This more general depiction of the molecule, versus detailing every atom in the molecule, is used to protect intellectual property. The company which applies for a patent makes a general claim for the usage of the molecule without revealing to their competitors the exact molecule for which they are declaring a useful application. History Markush structures are named after Eugene A. Markush, founder of the Pharma Chemical Corporation in New Jersey. He was involved in a legal case that set a precedent for g ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Line Notation
Line notation is a typographical notation system using ASCII characters, most often used for chemical nomenclature. Chemistry * Cell notation for representation of an electrochemical cell * Dyson / IUPAC (1944) * Hayward (1961) * International Chemical Identifier (InChI) * Wiswesser Line Notation (WLN) (1952) * Simplified molecular input line entry specification (SMILES) * Smiles arbitrary target specification (SMARTS) * SYBYL Line Notation (SLN) Mathematics * Mathematical markup language Music * GUIDO music notation Chess * Forsyth–Edwards Notation Forsyth–Edwards Notation (FEN) is a standard Chess notation, notation for describing a particular board position of a chess game. The purpose of FEN is to provide all the necessary information to restart a game from a particular position. FEN i ... {{DEFAULTSORT:Line Notation Notation Chemical nomenclature Musical notation ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
