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Self-consistent Mean Field (biology)
The self-consistent mean field (SCMF) method is an adaptation of mean field theory used in protein structure prediction to determine the optimal amino acid side chain packing given a fixed protein backbone. It is faster but less accurate than dead-end elimination and is generally used in situations where the protein of interest is too large for the problem to be tractable by DEE. General principles Like dead-end elimination, the SCMF method explores conformational space by discretizing the dihedral angles of each side chain into a set of rotamers for each position in the protein sequence. The method iteratively develops a probabilistic description of the relative population of each possible rotamer at each position, and the probability of a given structure is defined as a function of the probabilities of its individual rotamer components. The basic requirements for an effective SCMF implementation are: # A well-defined finite set of discrete independent variables # A precomputed ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Mean Field Theory
In physics and probability theory, Mean-field theory (MFT) or Self-consistent field theory studies the behavior of high-dimensional random (stochastic) models by studying a simpler model that approximates the original by averaging over degrees of freedom (the number of values in the final calculation of a statistic that are free to vary). Such models consider many individual components that interact with each other. The main idea of MFT is to replace all interactions to any one body with an average or effective interaction, sometimes called a ''molecular field''. This reduces any many-body problem into an effective one-body problem. The ease of solving MFT problems means that some insight into the behavior of the system can be obtained at a lower computational cost. MFT has since been applied to a wide range of fields outside of physics, including statistical inference, graphical models, neuroscience, artificial intelligence, epidemic models, queueing theory, computer-network p ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Structure Prediction
Protein structure prediction is the inference of the three-dimensional structure of a protein from its amino acid sequence—that is, the prediction of its secondary and tertiary structure from primary structure. Structure prediction is different from the inverse problem of protein design. Protein structure prediction is one of the most important goals pursued by computational biology; and it is important in medicine (for example, in drug design) and biotechnology (for example, in the design of novel enzymes). Starting in 1994, the performance of current methods is assessed biannually in the CASP experiment (Critical Assessment of Techniques for Protein Structure Prediction). A continuous evaluation of protein structure prediction web servers is performed by the community project CAMEO3D. Protein structure and terminology Proteins are chains of amino acids joined together by peptide bonds. Many conformations of this chain are possible due to the rotation of the main chain abou ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Amino Acid
Amino acids are organic compounds that contain both amino and carboxylic acid functional groups. Although hundreds of amino acids exist in nature, by far the most important are the alpha-amino acids, which comprise proteins. Only 22 alpha amino acids appear in the genetic code. Amino acids can be classified according to the locations of the core structural functional groups, as Alpha and beta carbon, alpha- , beta- , gamma- or delta- amino acids; other categories relate to Chemical polarity, polarity, ionization, and side chain group type (aliphatic, Open-chain compound, acyclic, aromatic, containing hydroxyl or sulfur, etc.). In the form of proteins, amino acid '' residues'' form the second-largest component (water being the largest) of human muscles and other tissues. Beyond their role as residues in proteins, amino acids participate in a number of processes such as neurotransmitter transport and biosynthesis. It is thought that they played a key role in enabling life ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Side Chain
In organic chemistry and biochemistry, a side chain is a chemical group that is attached to a core part of the molecule called the "main chain" or backbone. The side chain is a hydrocarbon branching element of a molecule that is attached to a larger hydrocarbon backbone. It is one factor in determining a molecule's properties and reactivity. A side chain is also known as a pendant chain, but a pendant group (side group) has a different definition. Conventions The placeholder R is often used as a generic placeholder for alkyl (saturated hydrocarbon) group side chains in chemical structure diagrams. To indicate other non-carbon groups in structure diagrams, X, Y, or Z are often used. History The ''R'' symbol was introduced by 19th-century French chemist Charles Frédéric Gerhardt, who advocated its adoption on the grounds that it would be widely recognizable and intelligible given its correspondence in multiple European languages to the initial letter of "root" or "residue": ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Tertiary Structure
Protein tertiary structure is the three dimensional shape of a protein. The tertiary structure will have a single polypeptide chain "backbone" with one or more protein secondary structures, the protein domains. Amino acid side chains may interact and bond in a number of ways. The interactions and bonds of side chains within a particular protein determine its tertiary structure. The protein tertiary structure is defined by its atomic coordinates. These coordinates may refer either to a protein domain or to the entire tertiary structure.Branden C. and Tooze J. "Introduction to Protein Structure" Garland Publishing, New York. 1990 and 1991. A number of tertiary structures may fold into a quaternary structure.Kyte, J. "Structure in Protein Chemistry." Garland Publishing, New York. 1995. History The science of the tertiary structure of proteins has progressed from one of hypothesis to one of detailed definition. Although Emil Fischer had suggested proteins were made of polypept ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Dead-end Elimination
The dead-end elimination algorithm (DEE) is a method for optimization (mathematics), minimizing a Function (mathematics), function over a discrete set of independent variables. The basic idea is to identify "dead ends", i.e., combinations of variables that are not necessary to define a global minimum because there is always a way of replacing such combination by a better or equivalent one. Then we can refrain from searching such combinations further. Hence, dead-end elimination is a mirror image of dynamic programming, in which "good" combinations are identified and explored further. Although the method itself is general, it has been developed and applied mainly to the problems of protein structure prediction, predicting and protein design, designing the structures of proteins. It closely related to the notion of dominance in optimization also known as substitutability in a Constraint Satisfaction Problem. The original description and proof of the dead-end elimination theorem can ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Dihedral Angle
A dihedral angle is the angle between two intersecting planes or half-planes. In chemistry, it is the clockwise angle between half-planes through two sets of three atoms, having two atoms in common. In solid geometry, it is defined as the union of a line and two half-planes that have this line as a common edge. In higher dimensions, a dihedral angle represents the angle between two hyperplanes. The planes of a flying machine are said to be at positive dihedral angle when both starboard and port main planes (commonly called wings) are upwardly inclined to the lateral axis. When downwardly inclined they are said to be at a negative dihedral angle. Mathematical background When the two intersecting planes are described in terms of Cartesian coordinates by the two equations : a_1 x + b_1 y + c_1 z + d_1 = 0 :a_2 x + b_2 y + c_2 z + d_2 = 0 the dihedral angle, \varphi between them is given by: :\cos \varphi = \frac and satisfies 0\le \varphi \le \pi/2. Alternatively, if an ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Rotamer
In chemistry, conformational isomerism is a form of stereoisomerism in which the isomers can be interconverted just by rotations about formally single bonds (refer to figure on single bond rotation). While any two arrangements of atoms in a molecule that differ by rotation about single bonds can be referred to as different conformations, conformations that correspond to local minima on the potential energy surface are specifically called conformational isomers or conformers. Conformations that correspond to local maxima on the energy surface are the transition states between the local-minimum conformational isomers. Rotations about single bonds involve overcoming a rotational energy barrier to interconvert one conformer to another. If the energy barrier is low, there is free rotation and a sample of the compound exists as a rapidly equilibrating mixture of multiple conformers; if the energy barrier is high enough then there is restricted rotation, a molecule may exist for a relati ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Boltzmann Distribution
In statistical mechanics and mathematics, a Boltzmann distribution (also called Gibbs distribution Translated by J.B. Sykes and M.J. Kearsley. See section 28) is a probability distribution or probability measure that gives the probability that a system will be in a certain state as a function of that state's energy and the temperature of the system. The distribution is expressed in the form: :p_i \propto e^ where is the probability of the system being in state , is the energy of that state, and a constant of the distribution is the product of the Boltzmann constant and thermodynamic temperature . The symbol \propto denotes proportionality (see for the proportionality constant). The term ''system'' here has a very wide meaning; it can range from a collection of 'sufficient number' of atoms or a single atom to a macroscopic system such as a natural gas storage tank. Therefore the Boltzmann distribution can be used to solve a very wide variety of problems. The distribu ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Simulated Annealing
Simulated annealing (SA) is a probabilistic technique for approximating the global optimum of a given function. Specifically, it is a metaheuristic to approximate global optimization in a large search space for an optimization problem. It is often used when the search space is discrete (for example the traveling salesman problem, the boolean satisfiability problem, protein structure prediction, and job-shop scheduling). For problems where finding an approximate global optimum is more important than finding a precise local optimum in a fixed amount of time, simulated annealing may be preferable to exact algorithms such as gradient descent or branch and bound. The name of the algorithm comes from annealing in metallurgy, a technique involving heating and controlled cooling of a material to alter its physical properties. Both are attributes of the material that depend on their thermodynamic free energy. Heating and cooling the material affects both the temperature and the the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Boltzmann Constant
The Boltzmann constant ( or ) is the proportionality factor that relates the average relative kinetic energy of particles in a gas with the thermodynamic temperature of the gas. It occurs in the definitions of the kelvin and the gas constant, and in Planck's law of black-body radiation and Boltzmann's entropy formula, and is used in calculating thermal noise in resistors. The Boltzmann constant has dimensions of energy divided by temperature, the same as entropy. It is named after the Austrian scientist Ludwig Boltzmann. As part of the 2019 redefinition of SI base units, the Boltzmann constant is one of the seven " defining constants" that have been given exact definitions. They are used in various combinations to define the seven SI base units. The Boltzmann constant is defined to be exactly . Roles of the Boltzmann constant Macroscopically, the ideal gas law states that, for an ideal gas, the product of pressure and volume is proportional to the product of amount of ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Applied Mathematics
Applied mathematics is the application of mathematical methods by different fields such as physics, engineering, medicine, biology, finance, business, computer science, and industry. Thus, applied mathematics is a combination of mathematical science and specialized knowledge. The term "applied mathematics" also describes the professional specialty in which mathematicians work on practical problems by formulating and studying mathematical models. In the past, practical applications have motivated the development of mathematical theories, which then became the subject of study in pure mathematics where abstract concepts are studied for their own sake. The activity of applied mathematics is thus intimately connected with research in pure mathematics. History Historically, applied mathematics consisted principally of applied analysis, most notably differential equations; approximation theory (broadly construed, to include representations, asymptotic methods, variational ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
