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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] |
Molecular Modeling
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 mec ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Binding Site
In biochemistry and molecular biology, a binding site is a region on a macromolecule such as a protein that binds to another molecule with specificity. The binding partner of the macromolecule is often referred to as a ligand. Ligands may include other proteins (resulting in a protein-protein interaction), enzyme substrates, second messengers, hormones, or allosteric modulators. The binding event is often, but not always, accompanied by a conformational change that alters the protein's function. Binding to protein binding sites is most often reversible (transient and non-covalent), but can also be covalent reversible or irreversible. Function Binding of a ligand to a binding site on protein often triggers a change in conformation in the protein and results in altered cellular function. Hence binding site on protein are critical parts of signal transduction pathways. Types of ligands include neurotransmitters, toxins, neuropeptides, and steroid hormones. Binding sites in ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Mechanics
Molecular mechanics uses classical mechanics to model molecular systems. The Born–Oppenheimer approximation is assumed valid and the potential energy of all systems is calculated as a function of the nuclear coordinates using force fields. Molecular mechanics can be used to study molecule systems ranging in size and complexity from small to large biological systems or material assemblies with many thousands to millions of atoms. All-atomistic molecular mechanics methods have the following properties: * Each atom is simulated as one particle * Each particle is assigned a radius (typically the van der Waals radius), polarizability, and a constant net charge (generally derived from quantum calculations and/or experiment) * Bonded interactions are treated as ''springs'' with an equilibrium distance equal to the experimental or calculated bond length Variants on this theme are possible. For example, many simulations have historically used a ''united-atom'' representation in which ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Search Algorithm
In computer science, a search algorithm is an algorithm designed to solve a search problem. Search algorithms work to retrieve information stored within particular data structure, or calculated in the search space of a problem domain, with either discrete or continuous values. algorithms are Although search engines use search algorithms, they belong to the study of information retrieval, not algorithmics. The appropriate search algorithm often depends on the data structure being searched, and may also include prior knowledge about the data. Search algorithms can be made faster or more efficient by specially constructed database structures, such as search trees, hash maps, and database indexes. Search algorithms can be classified based on their mechanism of searching into three types of algorithms: linear, binary, and hashing. Linear search algorithms check every record for the one associated with a target key in a linear fashion. Binary, or half-interval, searches repeatedly ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Homology Modeling
Homology modeling, also known as comparative modeling of protein, refers to constructing an atomic-resolution model of the "''target''" protein from its amino acid sequence and an experimental three-dimensional structure of a related homologous protein (the "''template''"). Homology modeling relies on the identification of one or more known protein structures likely to resemble the structure of the query sequence, and on the production of an alignment that maps residues in the query sequence to residues in the template sequence. It has been seen that protein structures are more conserved than protein sequences amongst homologues, but sequences falling below a 20% sequence identity can have very different structure. Evolutionarily related proteins have similar sequences and naturally occurring homologous proteins have similar protein structure. It has been shown that three-dimensional protein structure is evolutionarily more conserved than would be expected on the basis of sequence ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cryogenic Electron Microscopy
Cryogenic electron microscopy (cryo-EM) is a cryomicroscopy technique applied on samples cooled to cryogenic temperatures. For biological specimens, the structure is preserved by embedding in an environment of vitreous ice. An aqueous sample solution is applied to a grid-mesh and plunge-frozen in liquid ethane or a mixture of liquid ethane and propane. While development of the technique began in the 1970s, recent advances in detector technology and software algorithms have allowed for the determination of biomolecular structures at near-atomic resolution. This has attracted wide attention to the approach as an alternative to X-ray crystallography or NMR spectroscopy for macromolecular structure determination without the need for crystallization. In 2017, the Nobel Prize in Chemistry was awarded to Jacques Dubochet, Joachim Frank, and Richard Henderson "for developing cryo-electron microscopy for the high-resolution structure determination of biomolecules in solution." ''Nature ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein NMR
Nuclear magnetic resonance spectroscopy of proteins (usually abbreviated protein NMR) is a field of structural biology in which NMR spectroscopy is used to obtain information about the structure and dynamics of proteins, and also nucleic acids, and their complexes. The field was pioneered by Richard R. Ernst and Kurt Wüthrich at the ETH, and by Ad Bax, Marius Clore, Angela Gronenborn at the NIH, and Gerhard Wagner at Harvard University, among others. Structure determination by NMR spectroscopy usually consists of several phases, each using a separate set of highly specialized techniques. The sample is prepared, measurements are made, interpretive approaches are applied, and a structure is calculated and validated. NMR involves the quantum-mechanical properties of the central core ("nucleus") of the atom. These properties depend on the local molecular environment, and their measurement provides a map of how the atoms are linked chemically, how close they are in space, and how rapid ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
X-ray Crystallography
X-ray crystallography is the experimental science determining the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to diffract into many specific directions. By measuring the angles and intensities of these diffracted beams, a crystallographer can produce a three-dimensional picture of the density of electrons within the crystal. From this electron density, the mean positions of the atoms in the crystal can be determined, as well as their chemical bonds, their crystallographic disorder, and various other information. Since many materials can form crystals—such as salts, metals, minerals, semiconductors, as well as various inorganic, organic, and biological molecules—X-ray crystallography has been fundamental in the development of many scientific fields. In its first decades of use, this method determined the size of atoms, the lengths and types of chemical bonds, and the atomic-scale differences among various mat ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Overview Docking
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Overview may refer to: * Overview article, an artícle that summarizes the current state of understanding on a topic * Overview map, generalised view of a geographic area See also * Summary (other) * Outline (list) * ''A Brief Overview'' * Overview and Scrutiny * Overview effect The overview effect is a cognitive shift reported by some astronauts while viewing the Earth from space. Researchers have characterized the effect as "a state of awe with self-transcendent qualities, precipitated by a particularly striking vis ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Solvent-accessible Surface Area
The accessible surface area (ASA) or solvent-accessible surface area (SASA) is the surface area of a biomolecule that is accessible to a solvent. Measurement of ASA is usually described in units of square angstroms (a standard unit of measurement in molecular biology). ASA was first described by Lee & Richards in 1971 and is sometimes called the Lee-Richards molecular surface. ASA is typically calculated using the 'rolling ball' algorithm developed by Shrake & Rupley in 1973. This algorithm uses a sphere (of solvent) of a particular radius to 'probe' the surface of the molecule. Methods of calculating ASA Shrake–Rupley algorithm The Shrake–Rupley algorithm is a numerical method that draws a mesh of points equidistant from each atom of the molecule and uses the number of these points that are solvent accessible to determine the surface area. The points are drawn at a water molecule's estimated radius beyond the van der Waals radius, which is effectively similar to ‘rolling ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Complementary Surface
A complement is something that completes something else. Complement may refer specifically to: The arts * Complement (music), an interval that, when added to another, spans an octave ** Aggregate complementation, the separation of pitch-class collections into complementary sets * Complementary color, in the visual arts Biology and medicine *Complement system (immunology), a cascade of proteins in the blood that form part of innate immunity *Complementary DNA, DNA reverse transcribed from a mature mRNA template *Complementarity (molecular biology), a property whereby double stranded nucleic acids pair with each other *Complementation (genetics), a test to determine if independent recessive mutant phenotypes are caused by mutations in the same gene or in different genes Grammar and linguistics * Complement (linguistics), a word or phrase having a particular syntactic role ** Subject complement, a word or phrase adding to a clause's subject after a linking verb * Phonetic comp ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Van Der Waals Surface
The Van der Waals surface of a molecule is an abstract representation or model of that molecule, illustrating where, in very rough terms, a surface might reside for the molecule based on the hard cutoffs of Van der Waals radii for individual atoms, and it represents a surface through which the molecule might be conceived as interacting with other molecules. Also referred to as a ''Van der Waals envelope,'' the Van der Waals surface is named for Johannes Diderik van der Waals, a Dutch theoretical physicist and thermodynamicist who developed theory to provide a liquid-gas equation of state that accounted for the non-zero volume of atoms and molecules, and on their exhibiting an attractive force when they interacted (theoretical constructions that also bear his name). Van der Waals surfaces are therefore a tool used in the abstract representations of molecules, whether accessed, as they were originally, via hand calculation, or via physical wood/plastic models, or now digitally, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
