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Hierarchical Editing Language For Macromolecules
The hierarchical editing language for macromolecules (HELM) is a method of describing complex biological molecules. It is a notation that is machine readable to render the composition and structure of peptides, proteins, oligonucleotides, and related small molecule linkers. HELM was developed by a consortium of pharmaceutical companies in what is known as the Pistoia Alliance. Development began in 2008. In 2012 the notation was published openly and for free. The HELM open source project can be found on GitHub. HELM The need for HELM became obvious as researchers began working on modeling and computational projects involving molecules and engineered biomolecules of this type. There was not a language to describe the entities in an accurate manner which described both the composition and the complex branching and structure common in these entity types. Protein sequences can describe larger proteins and chemical language files such as mol files can describe simple peptides. But the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Peptides
Peptides (, ) are short chains of amino acids linked by peptide bonds. Long chains of amino acids are called proteins. Chains of fewer than twenty amino acids are called oligopeptides, and include dipeptides, tripeptides, and tetrapeptides. A polypeptide is a longer, continuous, unbranched peptide chain. Hence, peptides fall under the broad chemical classes of biological polymers and oligomers, alongside nucleic acids, oligosaccharides, polysaccharides, and others. A polypeptide that contains more than approximately 50 amino acids is known as a protein. Proteins consist of one or more polypeptides arranged in a biologically functional way, often bound to ligands such as coenzymes and cofactors, or to another protein or other macromolecule such as DNA or RNA, or to complex macromolecular assemblies. Amino acids that have been incorporated into peptides are termed residues. A water molecule is released during formation of each amide bond.. All peptides except cyclic pept ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
International Chemical Identifier
The International Chemical Identifier (InChI or ) 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 a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Encodings
In communications and information processing, code is a system of rules to convert information—such as a letter, word, sound, image, or gesture—into another form, sometimes shortened or secret, for communication through a communication channel or storage in a storage medium. An early example is an invention of language, which enabled a person, through speech, to communicate what they thought, saw, heard, or felt to others. But speech limits the range of communication to the distance a voice can carry and limits the audience to those present when the speech is uttered. The invention of writing, which converted spoken language into visual symbols, extended the range of communication across space and time. The process of encoding converts information from a source into symbols for communication or storage. Decoding is the reverse process, converting code symbols back into a form that the recipient understands, such as English or/and Spanish. One reason for coding is to en ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Chemical Nomenclature
A chemical nomenclature is a set of rules to generate systematic names for chemical compounds. The nomenclature used most frequently worldwide is the one created and developed by the International Union of Pure and Applied Chemistry (IUPAC). The IUPAC's rules for naming organic and inorganic compounds are contained in two publications, known as the '' Blue Book''. . and the '' Red Book'',. respectively. A third publication, known as the '' Green Book'',. recommends the use of symbols for physical quantities (in association with the IUPAP), while a fourth, the '' Gold Book'',''Compendium of Chemical Terminology, IMPACT Recommendations (2nd Ed.)'', Oxford:Blackwell Scientific Publications. (1997) defines many technical terms used in chemistry. Similar compendia exist for biochemistry''Biochemical Nomenclature and Related Documents'', London: Portland Press, 1992. (the ''White Book'', in association with the IUBMB), analytical chemistry (the '' Orange Book''), macromolecular che ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
FASTA
FASTA is a DNA and protein sequence alignment software package first described by David J. Lipman and William R. Pearson in 1985. Its legacy is the FASTA format which is now ubiquitous in bioinformatics. History The original FASTA program was designed for protein sequence similarity searching. Because of the exponentially expanding genetic information and the limited speed and memory of computers in the 1980s heuristic methods were introduced aligning a query sequence to entire data-bases. FASTA, published in 1987, added the ability to do DNA:DNA searches, translated protein:DNA searches, and also provided a more sophisticated shuffling program for evaluating statistical significance. There are several programs in this package that allow the alignment of protein sequences and DNA sequences. Nowadays, increased computer performance makes it possible to perform searches for local alignment detection in a database using the Smith–Waterman algorithm. FASTA is pronounced "f ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Graphics
Molecular graphics is the discipline and philosophy of studying molecules and their properties through graphical representation. IUPAC limits the definition to representations on a "graphical display device". Ever since Dalton's atoms and Kekulé's benzene, there has been a rich history of hand-drawn atoms and molecules, and these representations have had an important influence on modern molecular graphics. Colour molecular graphics are often used on chemistry journal covers artistically. History Prior to the use of computer graphics in representing molecular structure, Robert Corey and Linus Pauling developed a system for representing atoms or groups of atoms from hard wood on a scale of 1 inch = 1 angstrom connected by a clamping device to maintain the molecular configuration. These early models also established the CPK coloring scheme that is still used today to differentiate the different types of atoms in molecular models (e.g. carbon = black, oxygen = red, nitrogen = blue ... [...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. CT File is an open format, BIOVIA publishes its specification. BIOVIA requires users to register to download the CTFile 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. The mol ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecule Editor
A molecule editor is a computer program for creating and modifying representations of chemical structures. Molecule editors can manipulate chemical structure representations in either a simulated two-dimensional space or three-dimensional space, via 2D computer graphics or 3D computer graphics, respectively. Two-dimensional output is used as illustrations or to query chemical databases. Three-dimensional output is used to build molecular models, usually as part of molecular modelling software packages. Database molecular editors such as Leatherface, RECAP, and Molecule Slicer allow large numbers of molecules to be modified automatically according to rules such as 'deprotonate carboxylic acids' or 'break exocyclic bonds' that can be specified by a user. Molecule editors typically support reading and writing at least one file format A file format is a Computer standard, standard way that information is encoded for storage in a computer file. It specifies how bits are used t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Query Language
The Molecular Query Language (MQL) was designed to allow more complex, problem-specific search methods in chemoinformatics. In contrast to the widely used SMARTS queries, MQL provides for the specification of spatial and physicochemical properties of atoms and bonds. Additionally, it can easily be extended to handle non-atom-based graphs, also known as "reduced feature" graphs. The query language is based on an extended Backus–Naur form In computer science, extended Backus–Naur form (EBNF) is a family of metasyntax notations, any of which can be used to express a context-free grammar. EBNF is used to make a formal description of a formal language such as a computer programmi ... (EBNF) using JavaCC. Notes and references * E. Proschak, J. K. Wegner, A. Schüller, G. Schneider, U. Fechner, ''Molecular Query Language (MQL)-A Context-Free Grammar for Substructure Matching'', J. Chem. Inf. Model., 2007, ''47'', 295-301. See also * SMARTS * International Chemical Identi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Novartis
Novartis AG is a Swiss-American multinational pharmaceutical corporation based in Basel, Switzerland and Cambridge, Massachusetts, United States (global research).name="novartis.com">https://www.novartis.com/research-development/research-locations It is one of the largest pharmaceutical companies in the world. Novartis manufactures the drugs clozapine (Clozaril), diclofenac (Voltaren; sold to GlaxoSmithKline in 2015 deal), carbamazepine (Tegretol), valsartan (Diovan), imatinib mesylate (Gleevec/Glivec), cyclosporine (Neoral/Sandimmune), letrozole (Femara), methylphenidate (Ritalin; production ceased 2020), terbinafine (Lamisil), deferasirox (Exjade), and others. In March 1996, the companies Ciba-Geigy and Sandoz merged to form Novartis; the pharmaceutical and agrochemical divisions of both companies formed Novartis as an independent entity. Other Ciba-Geigy and Sandoz businesses were sold, or, like Ciba Specialty Chemicals, spun off as independent companies. The ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Proteins
Proteins are large biomolecules and macromolecules that comprise one or more long chains of amino acid residues. Proteins perform a vast array of functions within organisms, including catalysing metabolic reactions, DNA replication, responding to stimuli, providing structure to cells and organisms, and transporting molecules from one location to another. Proteins differ from one another primarily in their sequence of amino acids, which is dictated by the nucleotide sequence of their genes, and which usually results in protein folding into a specific 3D structure that determines its activity. A linear chain of amino acid residues is called a polypeptide. A protein contains at least one long polypeptide. Short polypeptides, containing less than 20–30 residues, are rarely considered to be proteins and are commonly called peptides. The individual amino acid residues are bonded together by peptide bonds and adjacent amino acid residues. The sequence of amino acid residues in ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
GlaxoSmithKline
GSK plc, formerly GlaxoSmithKline plc, is a British Multinational corporation, multinational pharmaceutical and biotechnology company with global headquarters in London, England. Established in 2000 by a Mergers and acquisitions, merger of Glaxo Wellcome and SmithKline Beecham. GSK is the tenth largest pharmaceutical company and #294 on the 2022 Fortune Global 500, ''Fortune'' Global 500, ranked behind other pharmaceutical companies China Resources, Sinopharm (company), Sinopharm, Johnson & Johnson, Pfizer, Roche, AbbVie, Novartis, Bayer, and Merck Group, Merck. The company has a primary listing on the London Stock Exchange and is a constituent of the FTSE 100 Index. , it had a market capitalisation of £70 billion, the eighth largest on the London Stock Exchange. It has a secondary listing on the New York Stock Exchange. The company developed the first malaria vaccine, RTS,S, which it said in 2014 it would make available for five percent above cost. Legacy products develope ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
