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.
DerivativeIn mathematics, the derivative shows the sensitivity of change of a function's output with respect to the input. Derivatives are a fundamental tool of calculus. For example, the derivative of the position of a moving object with respect to time is the object's velocity: this measures how quickly the position of the object changes when time advances. The derivative of a function of a single variable at a chosen input value, when it exists, is the slope of the tangent line to the graph of the function at that point.
Partial derivativeIn mathematics, a partial derivative of a function of several variables is its derivative with respect to one of those variables, with the others held constant (as opposed to the total derivative, in which all variables are allowed to vary). Partial derivatives are used in vector calculus and differential geometry. The partial derivative of a function with respect to the variable is variously denoted by It can be thought of as the rate of change of the function in the -direction.
AlkeneIn organic chemistry, an alkene is a hydrocarbon containing a carbon–carbon double bond. The double bond may be internal or in the terminal position. Terminal alkenes are also known as α-olefins. The International Union of Pure and Applied Chemistry (IUPAC) recommends using the name "alkene" only for acyclic hydrocarbons with just one double bond; alkadiene, alkatriene, etc., or polyene for acyclic hydrocarbons with two or more double bonds; cycloalkene, cycloalkadiene, etc.
Structural linguisticsStructural linguistics, or structuralism, in linguistics, denotes schools or theories in which language is conceived as a self-contained, self-regulating semiotic system whose elements are defined by their relationship to other elements within the system. It is derived from the work of Swiss linguist Ferdinand de Saussure and is part of the overall approach of structuralism. Saussure's Course in General Linguistics, published posthumously in 1916, stressed examining language as a dynamic system of interconnected units.
Molecular dynamicsMolecular dynamics (MD) is a computer simulation method for analyzing the physical movements of atoms and molecules. The atoms and molecules are allowed to interact for a fixed period of time, giving a view of the dynamic "evolution" of the system. In the most common version, the trajectories of atoms and molecules are determined by numerically solving Newton's equations of motion for a system of interacting particles, where forces between the particles and their potential energies are often calculated using interatomic potentials or molecular mechanical force fields.
Scoring functions for dockingIn the fields of computational chemistry and molecular modelling, scoring functions are mathematical functions used to approximately predict the binding affinity between two molecules after they have been docked. Most commonly one of the molecules is a small organic compound such as a drug and the second is the drug's biological target such as a protein receptor. Scoring functions have also been developed to predict the strength of intermolecular interactions between two proteins or between protein and DNA.
StructuralismIn sociology, anthropology, archaeology, history, philosophy, and linguistics, structuralism is a general theory of culture and methodology that implies that elements of human culture must be understood by way of their relationship to a broader system. It works to uncover the structures that underlie all the things that humans do, think, perceive, and feel. Alternatively, as summarized by philosopher Simon Blackburn, structuralism is:[T]he belief that phenomena of human life are not intelligible except through their interrelations.
Total derivativeIn mathematics, the total derivative of a function f at a point is the best linear approximation near this point of the function with respect to its arguments. Unlike partial derivatives, the total derivative approximates the function with respect to all of its arguments, not just a single one. In many situations, this is the same as considering all partial derivatives simultaneously. The term "total derivative" is primarily used when f is a function of several variables, because when f is a function of a single variable, the total derivative is the same as the ordinary derivative of the function.
Generalizations of the derivativeIn mathematics, the derivative is a fundamental construction of differential calculus and admits many possible generalizations within the fields of mathematical analysis, combinatorics, algebra, geometry, etc. The Fréchet derivative defines the derivative for general normed vector spaces . Briefly, a function , an open subset of , is called Fréchet differentiable at if there exists a bounded linear operator such that Functions are defined as being differentiable in some open neighbourhood of , rather than at individual points, as not doing so tends to lead to many pathological counterexamples.
Molecular biologyMolecular biology məˈlɛkjʊlər is the study of chemical and physical structure of biological macromolecules. It is a branch of biology that seeks to understand the molecular basis of biological activity in and between cells, including biomolecular synthesis, modification, mechanisms, and interactions. Molecular biology was first described as an approach focused on the underpinnings of biological phenomena—uncovering the structures of biological molecules as well as their interactions, and how these interactions explain observations of classical biology.
Logarithmic derivativeIn mathematics, specifically in calculus and complex analysis, the logarithmic derivative of a function f is defined by the formula where is the derivative of f. Intuitively, this is the infinitesimal relative change in f; that is, the infinitesimal absolute change in f, namely scaled by the current value of f. When f is a function f(x) of a real variable x, and takes real, strictly positive values, this is equal to the derivative of ln(f), or the natural logarithm of f.
Structural functionalismStructural functionalism, or simply functionalism, is "a framework for building theory that sees society as a complex system whose parts work together to promote solidarity and stability". This approach looks at society through a macro-level orientation, which is a broad focus on the social structures that shape society as a whole, and believes that society has evolved like organisms. This approach looks at both social structure and social functions.
Syn and anti additionIn organic chemistry, syn- and anti-addition are different ways in which substituent molecules can be added to an alkene () or alkyne (). The concepts of syn and anti addition are used to characterize the different reactions of organic chemistry by reflecting the stereochemistry of the products in a reaction. The type of addition that occurs depends on multiple different factors of a reaction, and is defined by the final orientation of the substituents on the parent molecule.
Structural anthropologyStructural anthropology is a school of sociocultural anthropology based on Claude Lévi-Strauss' 1949 idea that immutable deep structures exist in all cultures, and consequently, that all cultural practices have homologous counterparts in other cultures, essentially that all cultures are equatable. Lévi-Strauss' approach arose in large part from dialectics expounded on by Marx and Hegel, though dialectics (as a concept) dates back to Ancient Greek philosophy.
Organic synthesisOrganic synthesis is a special branch of chemical synthesis and is concerned with the intentional construction of organic compounds. Organic molecules are often more complex than inorganic compounds, and their synthesis has developed into one of the most important branches of organic chemistry. There are several main areas of research within the general area of organic synthesis: total synthesis, semisynthesis, and methodology.
Wirtinger derivativesIn complex analysis of one and several complex variables, Wirtinger derivatives (sometimes also called Wirtinger operators), named after Wilhelm Wirtinger who introduced them in 1927 in the course of his studies on the theory of functions of several complex variables, are partial differential operators of the first order which behave in a very similar manner to the ordinary derivatives with respect to one real variable, when applied to holomorphic functions, antiholomorphic functions or simply differentiabl
Total synthesisTotal synthesis is the complete chemical synthesis of a complex molecule, often a natural product, from simple, commercially-available precursors. It usually refers to a process not involving the aid of biological processes, which distinguishes it from semisynthesis. Syntheses may sometimes conclude at a precursor with further known synthetic pathways to a target molecule, in which case it is known as a formal synthesis. Total synthesis target molecules can be natural products, medicinally-important active ingredients, known intermediates, or molecules of theoretical interest.
Danishefsky Taxol total synthesisThe Danishefsky Taxol total synthesis in organic chemistry is an important third Taxol synthesis published by the group of Samuel Danishefsky in 1996 two years after the first two efforts described in the Holton Taxol total synthesis and the Nicolaou Taxol total synthesis. Combined they provide a good insight in the application of organic chemistry in total synthesis. Danishefsky's route to Taxol has many similarities with that of Nicolaou. Both are examples of convergent synthesis with a coupling of the A and the C ring from two precursors.
Wender Taxol total synthesisWender Taxol total synthesis in organic chemistry describes a Taxol total synthesis (one of six to date) by the group of Paul Wender at Stanford University published in 1997. This synthesis has much in common with the Holton Taxol total synthesis in that it is a linear synthesis starting from a naturally occurring compound with ring construction in the order A,B,C,D. The Wender effort is shorter by approximately 10 steps. Raw materials for the preparation of Taxol by this route include verbenone, prenyl bromine, allyl bromide, propiolic acid, Gilman reagent, and Eschenmoser's salt.
