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Chemical Similarity
Chemical similarity (or molecular similarity) refers to the similarity of chemical elements, molecules or chemical compounds with respect to either structural or functional qualities, i.e. the effect that the chemical compound has on reaction partners in inorganic or biological settings. Biological effects and thus also similarity of effects are usually quantified using the biological activity of a compound. In general terms, function can be related to the chemical activity of compounds (among others). The notion of ''chemical similarity'' (or ''molecular similarity'') is one of the most important concepts in cheminformatics. It plays an important role in modern approaches to predicting the properties of chemical compounds, designing chemicals with a predefined set of properties and, especially, in conducting drug design studies by screening large databases containing structures of available (or potentially available) chemicals. These studies are based on the similar property pri ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Chemical Element
A chemical element is a species of atoms that have a given number of protons in their nuclei, including the pure substance consisting only of that species. Unlike chemical compounds, chemical elements cannot be broken down into simpler substances by any chemical reaction. The number of protons in the nucleus is the defining property of an element, and is referred to as its atomic number (represented by the symbol ''Z'') – all atoms with the same atomic number are atoms of the same element. Almost all of the baryonic matter of the universe is composed of chemical elements (among rare exceptions are neutron stars). When different elements undergo chemical reactions, atoms are rearranged into new compounds held together by chemical bonds. Only a minority of elements, such as silver and gold, are found uncombined as relatively pure native element minerals. Nearly all other naturally occurring elements occur in the Earth as compounds or mixtures. Air is primarily a mixture o ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Journal Of Cheminformatics
The ''Journal of Cheminformatics'' is a peer-reviewed open access scientific journal that covers cheminformatics and molecular modelling. It was established in 2009 with David Wild (Indiana University) and Christoph Steinbeck (then at EMBL-EBI) as founding editors-in-chief, and was originally published by Chemistry Central. At the end of 2015, the Chemistry Central brand was retired and its titles, including ''Journal of Cheminformatics'', were merged with the SpringerOpen portfolio of open access journals. , the editors-in-chief are Rajarshi Guha (National Center for Advancing Translational Sciences) and Egon Willighagen (Maastricht University). The journal has issued a few special issues ("article collections") in 2011 and 2012, covering topics like PubChem3D, the Resource Description Framework, and the International Chemical Identifier. In June 2021 Willighagen announced his intention to step down at the end of the year, explaining in an open letter that the publisher Springer ... [...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] |
Drug Design
Drug design, often referred to as rational drug design or simply rational design, is the inventive process of finding new medications based on the knowledge of a biological target. The drug is most commonly an organic small molecule that activates or inhibits the function of a biomolecule such as a protein, which in turn results in a therapeutic benefit to the patient. In the most basic sense, drug design involves the design of molecules that are complementary in shape and charge to the biomolecular target with which they interact and therefore will bind to it. Drug design frequently but not necessarily relies on computer modeling techniques. This type of modeling is sometimes referred to as computer-aided drug design. Finally, drug design that relies on the knowledge of the three-dimensional structure of the biomolecular target is known as structure-based drug design. In addition to small molecules, biopharmaceuticals including peptides and especially therapeutic antibodies a ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Me-too Compound
The term "me-too drug" or "follow-on drug" refers to a medication that is similar to a pre-existing drug, usually by making minor modifications to the prototype, reflected in slight changes in the profiles of side effects or activity, and used to treat conditions for which drugs already exist. While pharmaceutical companies have justified the development of me-toos as offering incremental improvements in efficacy, side-effects, compliance and cost, critics have questioned the increasing marketing of me-toos, their absorption of research and development resources and their impact on the innovation of new treatments. In 1956, Louis S. Goodman, co‐editor of '' Goodman and Gilman'', referred to “the problem of the introduction of ‘me too’ drugs, that is, drugs without signal advantage of any sort”. However, me-too drugs can be novel compounds themselves. They are commonly used and include several beta blockers, antidepressants and stomach acid reducing and cholesterol lowe ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Drug Target
A biological target is anything within a living organism to which some other entity (like an endogenous ligand (biochemistry), ligand or a drug) is directed and/or binds, resulting in a change in its behavior or function. Examples of common classes of biological targets are proteins and nucleic acids. The definition is context-dependent, and can refer to the biological target of a pharmacological activity, pharmacologically active drug Chemical compound, compound, the receptor target of a hormone (like insulin), or some other target of an external stimulus. Biological targets are most commonly proteins such as enzymes, ion channels, and receptor (biochemistry), receptors. Mechanism The external stimulus (''i.e.'', the drug or ligand) physically binds to ("hits") the biological target. The interaction between the substance and the target may be: * noncovalent bonding, noncovalent – A relatively weak interaction between the stimulus and the target where no chemical bond is forme ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Chemical Space
Chemical space is a concept in cheminformatics referring to the property space spanned by all possible molecules and chemical compounds adhering to a given set of construction principles and boundary conditions. It contains millions of compounds which are readily accessible and available to researchers. It is a library used in the method of molecular Docking (molecular), docking. Theoretical spaces A chemical space often referred to in cheminformatics is that of potential pharmacologically active molecules. Its size is estimated to be in the order of 1060 molecules. There are no rigorous methods for determining the precise size of this space. The assumptions used for estimating the number of potential pharmacologically active molecules, however, use the Lipinski's rule of five, Lipinski rules, in particular the molecular weight limit of 500. The estimate also restricts the chemical elements used to be Carbon, Hydrogen, Oxygen, Nitrogen and Sulfur. It further makes the assumption of ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Graph Theory
In mathematics, graph theory is the study of ''graphs'', which are mathematical structures used to model pairwise relations between objects. A graph in this context is made up of '' vertices'' (also called ''nodes'' or ''points'') which are connected by '' edges'' (also called ''links'' or ''lines''). A distinction is made between undirected graphs, where edges link two vertices symmetrically, and directed graphs, where edges link two vertices asymmetrically. Graphs are one of the principal objects of study in discrete mathematics. Definitions Definitions in graph theory vary. The following are some of the more basic ways of defining graphs and related mathematical structures. Graph In one restricted but very common sense of the term, a graph is an ordered pair G=(V,E) comprising: * V, a set of vertices (also called nodes or points); * E \subseteq \, a set of edges (also called links or lines), which are unordered pairs of vertices (that is, an edge is associated with t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Network Theory
Network theory is the study of graphs as a representation of either symmetric relations or asymmetric relations between discrete objects. In computer science and network science, network theory is a part of graph theory: a network can be defined as a graph in which nodes and/or edges have attributes (e.g. names). Network theory has applications in many disciplines including statistical physics, particle physics, computer science, electrical engineering, biology, archaeology, economics, finance, operations research, climatology, ecology, public health, sociology, and neuroscience. Applications of network theory include logistical networks, the World Wide Web, Internet, gene regulatory networks, metabolic networks, social networks, epistemological networks, etc.; see List of network theory topics for more examples. Euler's solution of the Seven Bridges of Königsberg problem is considered to be the first true proof in the theory of networks. Network optimization Network pr ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Jaccard Index
The Jaccard index, also known as the Jaccard similarity coefficient, is a statistic used for gauging the similarity and diversity of sample sets. It was developed by Grove Karl Gilbert in 1884 as his ratio of verification (v) and now is frequently referred to as the Critical Success Index in meteorology. It was later developed independently by Paul Jaccard, originally giving the French name ''coefficient de communauté'', and independently formulated again by T. Tanimoto. Thus, the Tanimoto index or Tanimoto coefficient are also used in some fields. However, they are identical in generally taking the ratio of Intersection over Union. The Jaccard coefficient measures similarity between finite sample sets, and is defined as the size of the intersection divided by the size of the union of the sample sets: : J(A,B) = = . Note that by design, 0\le J(A,B)\le 1. If ''A'' intersection ''B'' is empty, then ''J''(''A'',''B'') = 0. The Jaccard coefficient is widely used in c ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Similarity Measure
In statistics and related fields, a similarity measure or similarity function or similarity metric is a real-valued function that quantifies the similarity between two objects. Although no single definition of a similarity exists, usually such measures are in some sense the inverse of distance metrics: they take on large values for similar objects and either zero or a negative value for very dissimilar objects. Though, in more broad terms, a similarity function may also satisfy metric axioms. Cosine similarity is a commonly used similarity measure for real-valued vectors, used in (among other fields) information retrieval to score the similarity of documents in the vector space model. In machine learning, common kernel functions such as the RBF kernel can be viewed as similarity functions. Use in clustering In spectral clustering, a similarity, or affinity, measure is used to transform data to overcome difficulties related to lack of convexity in the shape of the data distribut ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Virtual Screening
Virtual screening (VS) is a computational technique used in drug discovery to search libraries of small molecules in order to identify those structures which are most likely to bind to a drug target, typically a protein receptor or enzyme. Virtual screening has been defined as "automatically evaluating very large libraries of compounds" using computer programs. As this definition suggests, VS has largely been a numbers game focusing on how the enormous chemical space of over 1060 conceivable compounds can be filtered to a manageable number that can be synthesized, purchased, and tested. Although searching the entire chemical universe may be a theoretically interesting problem, more practical VS scenarios focus on designing and optimizing targeted combinatorial libraries and enriching libraries of available compounds from in-house compound repositories or vendor offerings. As the accuracy of the method has increased, virtual screening has become an integral part of the drug discove ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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