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Katchalski-Katzir Algorithm
The Katchalski-Katzir algorithm is an algorithm for docking of rigid molecules, developed by Ephraim Katchalski-Katzir, Isaac Shariv and Miriam Eisenstein. In 1990 Professor Ephraim Katchalski-Katzir, former president of the state of Israel, gathered a group of physicists, chemists and biologists at the Weizmann Institute of Science, to discuss intermolecular recognition. One of the outcomes of these discussions was the Katchalski-Katzir Algorithm, proposed by Dr. Isaac Shariv, a physics PhD student at the time. The Algorithm was implemented in a computer program, MolFit, by Dr. Miriam Eisenstein from the department of Structural Chemistry. It is a purely geometric algorithm, but some extensions of it also implement electrostatics. The algorithm's first step is mapping the molecules onto grids, with each point of a grid being marked as either: * outside the molecule * on the molecule's surface * inside the molecule The algorithm increases the surface contact and minimizes volum ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Docking (molecular)
In the field of molecular modeling, docking is a method which predicts the preferred orientation of one molecule to a second when a ligand and a target are bound to each other to form a stable complex. Knowledge of the preferred orientation in turn may be used to predict the strength of association or binding affinity between two molecules using, for example, scoring functions. The associations between biologically relevant molecules such as proteins, peptides, nucleic acids, carbohydrates, and lipids play a central role in signal transduction. Furthermore, the relative orientation of the two interacting partners may affect the type of signal produced (e.g., agonism vs antagonism). Therefore, docking is useful for predicting both the strength and type of signal produced. Molecular docking is one of the most frequently used methods in structure-based drug design, due to its ability to predict the binding-conformation of small molecule ligands to the appropriate target bind ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ephraim Katzir
Ephraim Katzir ( he, אפרים קציר, translit=Efrayim Katsir; – 30 May 2009) was an Israeli biophysics, biophysicist and Israeli Labor Party, Labor Party politician. He was the List of Presidents of Israel, fourth President of Israel from 1973 until 1978. Biography Efraim Katchalski (later Katzir) was the son of Yudel-Gersh (Yehuda) and Tzilya Katchalski,Запис про народження 3 травня (ст. ст.) 1916 року Ефраїма Качальського в метричній книзі київського рабинату // Central State Historical Archives of Ukraine in Kyiv, ЦДІ ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Weizmann Institute Of Science
The Weizmann Institute of Science ( he, מכון ויצמן למדע ''Machon Vaitzman LeMada'') is a public research university in Rehovot, Israel, established in 1934, 14 years before the State of Israel. It differs from other Israeli universities in that it offers only postgraduate degrees in the natural and exact sciences. It is a multidisciplinary research center, with around 3,800 scientists, postdoctoral fellows, Ph.D. and M.Sc. students, and scientific, technical, and administrative staff working at the institute. As of 2019, six Nobel laureates and three Turing Award winners have been associated with the Weizmann Institute of Science. History Founded in 1934 by Chaim Weizmann and his first team, among them Benjamin M. Bloch, as the Daniel Sieff Research Institute. Weizmann had offered the post of director to Nobel Prize laureate Fritz Haber, but took over the directorship himself after Haber's death en route to Palestine. Before he became President of the State o ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Electrostatics
Electrostatics is a branch of physics that studies electric charges at rest (static electricity). Since classical times, it has been known that some materials, such as amber, attract lightweight particles after rubbing. The Greek word for amber, (), was thus the source of the word 'electricity'. Electrostatic phenomena arise from the forces that electric charges exert on each other. Such forces are described by Coulomb's law. Even though electrostatically induced forces seem to be rather weak, some electrostatic forces are relatively large. The force between an electron and a proton, which together make up a hydrogen atom, is about 36 orders of magnitude stronger than the gravitational force acting between them. There are many examples of electrostatic phenomena, from those as simple as the attraction of plastic wrap to one's hand after it is removed from a package, to the apparently spontaneous explosion of grain silos, the damage of electronic components during manufacturin ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Fast Fourier Transform
A fast Fourier transform (FFT) is an algorithm that computes the discrete Fourier transform (DFT) of a sequence, or its inverse (IDFT). Fourier analysis converts a signal from its original domain (often time or space) to a representation in the frequency domain and vice versa. The DFT is obtained by decomposing a sequence of values into components of different frequencies. This operation is useful in many fields, but computing it directly from the definition is often too slow to be practical. An FFT rapidly computes such transformations by factorizing the DFT matrix into a product of sparse (mostly zero) factors. As a result, it manages to reduce the complexity of computing the DFT from O\left(N^2\right), which arises if one simply applies the definition of DFT, to O(N \log N), where N is the data size. The difference in speed can be enormous, especially for long data sets where ''N'' may be in the thousands or millions. In the presence of round-off error, many FFT algorithm ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Electrostatic
Electrostatics is a branch of physics that studies electric charges at rest (static electricity). Since classical times, it has been known that some materials, such as amber, attract lightweight particles after rubbing. The Greek word for amber, (), was thus the source of the word 'electricity'. Electrostatic phenomena arise from the forces that electric charges exert on each other. Such forces are described by Coulomb's law. Even though electrostatically induced forces seem to be rather weak, some electrostatic forces are relatively large. The force between an electron and a proton, which together make up a hydrogen atom, is about 36 orders of magnitude stronger than the gravitational force acting between them. There are many examples of electrostatic phenomena, from those as simple as the attraction of plastic wrap to one's hand after it is removed from a package, to the apparently spontaneous explosion of grain silos, the damage of electronic components during manufacturi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Hydrophobic
In chemistry, hydrophobicity is the physical property of a molecule that is seemingly repelled from a mass of water (known as a hydrophobe). In contrast, hydrophiles are attracted to water. Hydrophobic molecules tend to be nonpolar and, thus, prefer other neutral molecules and nonpolar solvents. Because water molecules are polar, hydrophobes do not dissolve well among them. Hydrophobic molecules in water often cluster together, forming micelles. Water on hydrophobic surfaces will exhibit a high contact angle. Examples of hydrophobic molecules include the alkanes, oils, fats, and greasy substances in general. Hydrophobic materials are used for oil removal from water, the management of oil spills, and chemical separation processes to remove non-polar substances from polar compounds. Hydrophobic is often used interchangeably with lipophilic, "fat-loving". However, the two terms are not synonymous. While hydrophobic substances are usually lipophilic, there are exceptions, suc ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Hydrophilic
A hydrophile is a molecule or other molecular entity that is attracted to water molecules and tends to be dissolved by water.Liddell, H.G. & Scott, R. (1940). ''A Greek-English Lexicon'' Oxford: Clarendon Press. In contrast, hydrophobes are not attracted to water and may seem to be repelled by it. Hygroscopics ''are'' attracted to water, but are not dissolved by water. Molecules A hydrophilic molecule or portion of a molecule is one whose interactions with water and other polar substances are more thermodynamically favorable than their interactions with oil or other hydrophobic solvents. They are typically charge-polarized and capable of hydrogen bonding. This makes these molecules soluble not only in water but also in other polar solvents. Hydrophilic molecules (and portions of molecules) can be contrasted with hydrophobic molecules (and portions of molecules). In some cases, both hydrophilic and hydrophobic properties occur in a single molecule. An example of these amphiph ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Induced Fit
Enzyme catalysis is the increase in the rate of a process by a biological molecule, an "enzyme". Most enzymes are proteins, and most such processes are chemical reactions. Within the enzyme, generally catalysis occurs at a localized site, called the active site. Most enzymes are made predominantly of proteins, either a single protein chain or many such chains in a multi-subunit complex. Enzymes often also incorporate non-protein components, such as metal ions or specialized organic molecules known as cofactor (e.g. adenosine triphosphate). Many cofactors are vitamins, and their role as vitamins is directly linked to their use in the catalysis of biological process within metabolism. Catalysis of biochemical reactions in the cell is vital since many but not all metabolically essential reactions have very low rates when uncatalysed. One driver of protein evolution is the optimization of such catalytic activities, although only the most crucial enzymes operate near catalytic e ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Convolution Theorem
In mathematics, the convolution theorem states that under suitable conditions the Fourier transform of a convolution of two functions (or signals) is the pointwise product of their Fourier transforms. More generally, convolution in one domain (e.g., time domain) equals point-wise multiplication in the other domain (e.g., frequency domain). Other versions of the convolution theorem are applicable to various Fourier-related transforms. Functions of a continuous variable Consider two functions g(x) and h(x) with Fourier transforms G and H: \begin G(f) &\triangleq \mathcal\(f) = \int_^g(x) e^ \, dx, \quad f \in \mathbb\\ H(f) &\triangleq \mathcal\(f) = \int_^h(x) e^ \, dx, \quad f \in \mathbb \end where \mathcal denotes the Fourier transform operator. The transform may be normalized in other ways, in which case constant scaling factors (typically 2\pi or \sqrt) will appear in the convolution theorem below. The convolution of g and h is defined by: r(x) = \(x) \triangleq \int_^ g(\t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Modelling
Molecular modelling encompasses all methods, theoretical and computational, used to model or mimic the behaviour of molecules. The methods are used in the fields of computational chemistry, drug design, computational biology and materials science to study molecular systems ranging from small chemical systems to large biological molecules and material assemblies. The simplest calculations can be performed by hand, but inevitably computers are required to perform molecular modelling of any reasonably sized system. The common feature of molecular modelling methods is the atomistic level description of the molecular systems. This may include treating atoms as the smallest individual unit (a molecular mechanics approach), or explicitly modelling protons and neutrons with its quarks, anti-quarks and gluons and electrons with its photons (a quantum chemistry approach). Molecular mechanics Molecular mechanics is one aspect of molecular modelling, as it involves the use of classical ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Computational Chemistry
Computational chemistry is a branch of chemistry that uses computer simulation to assist in solving chemical problems. It uses methods of theoretical chemistry, incorporated into computer programs, to calculate the structures and properties of molecules, groups of molecules, and solids. It is essential because, apart from relatively recent results concerning the hydrogen molecular ion (dihydrogen cation, see references therein for more details), the quantum many-body problem cannot be solved analytically, much less in closed form. While computational results normally complement the information obtained by chemical experiments, it can in some cases predict hitherto unobserved chemical phenomena. It is widely used in the design of new drugs and materials. Examples of such properties are structure (i.e., the expected positions of the constituent atoms), absolute and relative (interaction) energies, electronic charge density distributions, dipoles and higher multipole moments, vi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
