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Molecule Mining
This page describes mining for 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\neqi) 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. Fröhlich, J. K. Wegner, A. Zell, ''Optimal Assignment Kernels For Attributed ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Small Molecule
Within the fields of molecular biology and pharmacology, a small molecule or micromolecule is a low molecular weight (≤ 1000 daltons) organic compound that may regulate a biological process, with a size on the order of 1 nm. Many drugs are small molecules; the terms are equivalent in the literature. Larger structures such as nucleic acids and proteins, and many polysaccharides are not small molecules, although their constituent monomers (ribo- or deoxyribonucleotides, amino acids, and monosaccharides, respectively) are often considered small molecules. Small molecules may be used as research tools to probe biological function as well as leads in the development of new therapeutic agents. Some can inhibit a specific function of a protein or disrupt protein–protein interactions. Pharmacology usually restricts the term "small molecule" to molecules that bind specific biological macromolecules and act as an effector, altering the activity or function of the target. Small ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cheminformatics
Cheminformatics (also known as chemoinformatics) refers to use of physical chemistry theory with computer and information science techniques—so called "''in silico''" techniques—in application to a range of descriptive and prescriptive problems in the field of chemistry, including in its applications to biology and related molecular fields. Such ''in silico'' techniques are used, for example, by pharmaceutical companies and in academic settings to aid and inform the process of drug discovery, for instance in the design of well-defined combinatorial libraries of synthetic compounds, or to assist in structure-based drug design. The methods can also be used in chemical and allied industries, and such fields as environmental science and pharmacology, where chemical processes are involved or studied. History Cheminformatics has been an active field in various guises since the 1970s and earlier, with activity in academic departments and commercial pharmaceutical research and dev ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Partition Coefficient
In the physical sciences, a partition coefficient (''P'') or distribution coefficient (''D'') is the ratio of concentrations of a compound in a mixture of two immiscible solvents at equilibrium. This ratio is therefore a comparison of the solubilities of the solute in these two liquids. The partition coefficient generally refers to the concentration ratio of un-ionized species of compound, whereas the distribution coefficient refers to the concentration ratio of all species of the compound (ionized plus un-ionized). In the chemical and pharmaceutical sciences, both phases usually are solvents. Most commonly, one of the solvents is water, while the second is hydrophobic, such as 1-octanol. Hence the partition coefficient measures how hydrophilic ("water-loving") or hydrophobic ("water-fearing") a chemical substance is. Partition coefficients are useful in estimating the distribution of drugs within the body. Hydrophobic drugs with high octanol-water partition coefficients are m ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
ADME
ADME is an abbreviation in pharmacokinetics and pharmacology for " absorption, distribution, metabolism, and excretion", and describes the disposition of a pharmaceutical compound within an organism. The four criteria all influence the drug levels and kinetics of drug exposure to the tissues and hence influence the performance and pharmacological activity of the compound as a drug. Sometimes, liberation and/or toxicity are also considered, yielding LADME, ADMET, or LADMET. Components Absorption/administration For a compound to reach a tissue, it usually must be taken into the bloodstream – often via mucous surfaces like the digestive tract (intestinal absorption) – before being taken up by the target cells. Factors such as poor compound solubility, gastric emptying time, intestinal transit time, chemical instability in the stomach, and inability to permeate the intestinal wall can all reduce the extent to which a drug is absorbed after oral administration. Absorptio ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Chemical Graph Theory
Chemical graph theory is the topology branch of mathematical chemistry which applies graph theory to mathematical modelling of chemical phenomena. The pioneers of chemical graph theory are Alexandru Balaban, Ante Graovac, Iván Gutman, Haruo Hosoya, Milan Randić and Nenad Trinajstić (also Harry Wiener and others). In 1988, it was reported that several hundred researchers worked in this area, producing about 500 articles annually. A number of monographs have been written in the area, including the two-volume comprehensive text by Trinajstić, ''Chemical Graph Theory'', that summarized the field up to mid-1980s. The adherents of the theory maintain that the properties of a chemical graph (i.e., a graph-theoretical representation of a molecule) give valuable insights into the chemical phenomena. Others contend that graphs play only a fringe role in chemical research.D.H. Rouvray, "Combinatorics in Chemistry", pp. 1955-1982, in: Ronald Graham, Martin Grötschel, László Lovász (E ... [...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 (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 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 we .. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Doklady Akademii Nauk SSSR
The ''Proceedings of the USSR Academy of Sciences'' (russian: Доклады Академии Наук СССР, ''Doklady Akademii Nauk SSSR'' (''DAN SSSR''), french: Comptes Rendus de l'Académie des Sciences de l'URSS) was a Soviet journal that was dedicated to publishing original, academic research papers in physics, mathematics, chemistry, geology, and biology. It was first published in 1933 and ended in 1992 with volume 322, issue 3. Today, it is continued by ''Doklady Akademii Nauk'' (russian: Доклады Академии Наук), which began publication in 1992. The journal is also known as the ''Proceedings of the Russian Academy of Sciences (RAS)''. ''Doklady'' has had a complicated publication and translation history. A number of translation journals exist which publish selected articles from the original by subject section; these are listed below. History The Russian Academy of Sciences dates from 1724, with a continuous series of variously named publications dat ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Small Molecule Subgraph Detector
Small may refer to: Science and technology * SMALL, an ALGOL-like programming language * Small (anatomy), the lumbar region of the back * ''Small'' (journal), a nano-science publication * <small>, an HTML element that defines smaller text Arts and entertainment Fictional characters * Small, in the British children's show Big & Small Other uses * Small, of little size * Small (surname) * "Small", a song from the album ''The Cosmos Rocks'' by Queen + Paul Rodgers See also * Smal (other) * List of people known as the Small The Small is an epithet applied to: *Bolko II the Small (c. 1312–1368), Duke of Świdnica, of Jawor and Lwówek, of Lusatia, over half of Brzeg and Oława, of Siewierz, and over half of Głogów and Ścinawa *Dionysius Exiguus (c. 470–c. 5 ... * Smalls (other) {{disambiguation ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Maximum Common Subgraph Isomorphism Problem
In graph theory and theoretical computer science, a maximum common subgraph may mean either: *Maximum common induced subgraph In graph theory and theoretical computer science, a maximum common induced subgraph of two graphs ''G'' and ''H'' is a graph that is an induced subgraph of both ''G'' and ''H'', and that has as many vertices as possible. Finding this graph is NP-ha ..., a graph that is an induced subgraph of two given graphs and has as many vertices as possible * Maximum common edge subgraph, a graph that is a subgraph of two given graphs and has as many edges as possible {{sia ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecule
A molecule is a group of two or more atoms held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions which 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 (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 bonds, are typically not consid ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
