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MDL Molfile
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] |
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 Bond
A chemical bond is the association of atoms or ions to form molecules, crystals, and other structures. The bond may result from the electrostatic force between oppositely charged ions as in ionic bonds or through the sharing of electrons as in covalent bonds, or some combination of these effects. Chemical bonds are described as having different strengths: there are "strong bonds" or "primary bonds" such as covalent, ionic and metallic bonds, and "weak bonds" or "secondary bonds" such as dipole–dipole interactions, the London dispersion force, and hydrogen bonding. Since opposite electric charges attract, the negatively charged electrons surrounding the nucleus and the positively charged protons within a nucleus attract each other. Electrons shared between two nuclei will be attracted to both of them. "Constructive quantum mechanical wavefunction interference" stabilizes the paired nuclei (see Theories of chemical bonding). Bonded nuclei maintain an optima ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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] |
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] |
InChI
The International Chemical Identifier (InChI, pronounced ) is a textual identifier for chemical substances, designed to provide a standard way to encode molecular information and to facilitate the search for such information in databases and on the web. Initially developed by the International Union of Pure and Applied Chemistry (IUPAC) and National Institute of Standards and Technology (NIST) from 2000 to 2005, the format and algorithms are non-proprietary. Since May 2009, it has been developed by the InChI Trust, a nonprofit charity from the United Kingdom which works to implement and promote the use of InChI. The identifiers describe chemical substances in terms of ''layers'' of information — the atoms and their bond connectivity, tautomeric information, isotope information, stereochemistry, and electronic charge information. Not all layers have to be provided; for instance, the tautomer layer can be omitted if that type of information is not relevant to the particular ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
SMILES
A smile is a facial expression formed primarily by flexing the muscles at the sides of the mouth. Some smiles include a contraction of the muscles at the corner of the eyes, an action known as a Duchenne smile. Among humans, a smile expresses delight, sociability, happiness, joy, or amusement. It is distinct from a similar but usually involuntary expression of anxiety known as a grimace. Although cross-cultural studies have shown that smiling is a means of communication throughout the world, there are large differences among different cultures, religions, and societies, with some using smiles to convey confusion, embarrassment, or awkwardness. Evolutionary background Primatologist Signe Preuschoft traces the smile back over 30 million years of evolution to a "fear grin" stemming from monkeys and apes, who often used barely clenched teeth to portray to predators that they were harmless or to signal submission to more dominant group members. The smile may have evolved differen ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Delimiter
A delimiter is a sequence of one or more Character (computing), characters for specifying the boundary between separate, independent regions in plain text, Expression (mathematics), mathematical expressions or other Data stream, data streams. An example of a delimiter is the comma character, which acts as a ''field delimiter'' in a sequence of comma-separated values. Another example of a delimiter is the time gap used to separate letters and words in the transmission of Morse code. In mathematics, delimiters are often used to specify the scope of an Operation (mathematics), operation, and can occur both as isolated symbols (e.g., Colon (punctuation), colon in "1 : 4") and as a pair of opposing-looking symbols (e.g., Angled bracket, angled brackets in \langle a, b \rangle). Delimiters represent one of various means of specifying boundaries in a data stream. String literal#Declarative notation, Declarative notation, for example, is an alternate method (without the use of delimiter ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molfile
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] |
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] |
Angstrom
The angstrom (; ) is a unit of length equal to m; that is, one ten-billionth of a metre, a hundred-millionth of a centimetre, 0.1 nanometre, or 100 picometres. The unit is named after the Swedish physicist Anders Jonas Ångström (1814–1874). It was originally spelled with Swedish letters, as Ångström and later as ångström (). The latter spelling is still listed in some dictionaries, but is now rare in English texts. Some popular US dictionaries list only the spelling ''angstrom''. The unit's symbol is Å, which is a letter of the Swedish alphabet, regardless of how the unit is spelled. However, "A" or "A.U." may be used in less formal contexts or typographically limited media. The angstrom is often used in the natural sciences and technology to express sizes of atoms, molecules, microscopic biological structures, and lengths of chemical bonds, arrangement of atoms in crystals, wavelengths of electromagnetic radiation, and dimensions of integrated circuit part ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
MDL Information Systems
MDL Information Systems, Inc. was a provider of R&D informatics products for the life sciences and chemicals industries. The company was launched as a computer-aided drug design firm (originally named Molecular Design Limited, Inc.) in January 1978 in Hayward, California. The company was acquired by Symyx Technologies, Inc. in 2007. Subsequently Accelrys merged with Symyx. The Accelrys name was retained for the combined company. In 2014 Accelrys was acquired by Dassault Systèmes. The Accelrys business unit was renamed BIOVIA. History Molecular Design Limited, Inc. was founded by Stuart Marson and W. Todd Wipke in 1978. With 15 years of research on computer synthesis at the University of California, Santa Cruz, Wipke, with Marson, fresh from a Ph.D. at Stanford University and a postdoctoral stint at the University of California, Berkeley, were convinced that computer-assisted molecular design was possible as a commercial enterprise.C&EN, June 18, 1979 Employee #3 was Stephen P ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
L-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 peptidogly ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
