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Structural Alignment
Structural alignment attempts to establish homology between two or more polymer structures based on their shape and three-dimensional conformation. This process is usually applied to protein tertiary structures but can also be used for large RNA molecules. In contrast to simple structural superposition, where at least some equivalent residues of the two structures are known, structural alignment requires no ''a priori'' knowledge of equivalent positions. Structural alignment is a valuable tool for the comparison of proteins with low sequence similarity, where evolutionary relationships between proteins cannot be easily detected by standard sequence alignment techniques. Structural alignment can therefore be used to imply evolutionary relationships between proteins that share very little common sequence. However, caution should be used in using the results as evidence for shared evolutionary ancestry because of the possible confounding effects of convergent evolution by which mul ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Alignment Of Thioredoxins2
Alignment may refer to: Archaeology * Alignment (archaeology), a co-linear arrangement of features or structures with external landmarks * Stone alignment, a linear arrangement of upright, parallel megalithic standing stones Biology * Structural alignment, establishing similarities in the 3D structure of protein molecules * Sequence alignment, in bioinformatics, arranging the sequences of DNA, RNA, or protein to identify similarities ** Alignment program, software used in sequence alignment Engineering * Road alignment, the route of a road, defined as a series of horizontal tangents and curves, as defined by planners and surveyors * Railway alignment, three-dimensional geometry of track layouts * Transfer alignment, a process for initializing and calibrating the inertial navigation system on a missile or torpedo * Shaft alignment, in mechanical engineering, aligning two or more shafts with each other * Wheel alignment, automobile wheel and suspension angles which affect ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Root Mean Square
In mathematics and its applications, the root mean square of a set of numbers x_i (abbreviated as RMS, or rms and denoted in formulas as either x_\mathrm or \mathrm_x) is defined as the square root of the mean square (the arithmetic mean of the squares) of the set. The RMS is also known as the quadratic mean (denoted M_2) and is a particular case of the generalized mean. The RMS of a continuously varying function (denoted f_\mathrm) can be defined in terms of an integral of the squares of the instantaneous values during a cycle. For alternating electric current, RMS is equal to the value of the constant direct current that would produce the same power dissipation in a resistive load. In estimation theory, the root-mean-square deviation of an estimator is a measure of the imperfection of the fit of the estimator to the data. Definition The RMS value of a set of values (or a continuous-time waveform) is the square root of the arithmetic mean of the squares of the values, or ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Quaternion
In mathematics, the quaternion number system extends the complex numbers. Quaternions were first described by the Irish mathematician William Rowan Hamilton in 1843 and applied to mechanics in three-dimensional space. Hamilton defined a quaternion as the quotient of two '' directed lines'' in a three-dimensional space, or, equivalently, as the quotient of two vectors. Multiplication of quaternions is noncommutative. Quaternions are generally represented in the form :a + b\ \mathbf i + c\ \mathbf j +d\ \mathbf k where , and are real numbers; and , and are the ''basic quaternions''. Quaternions are used in pure mathematics, but also have practical uses in applied mathematics, particularly for calculations involving three-dimensional rotations, such as in three-dimensional computer graphics, computer vision, and crystallographic texture analysis. They can be used alongside other methods of rotation, such as Euler angles and rotation matrices, or as an alternative to th ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Hydrogen Bond
In chemistry, a hydrogen bond (or H-bond) is a primarily electrostatic force of attraction between a hydrogen (H) atom which is covalently bound to a more electronegative "donor" atom or group (Dn), and another electronegative atom bearing a lone pair of electrons—the hydrogen bond acceptor (Ac). Such an interacting system is generally denoted , where the solid line denotes a polar covalent bond, and the dotted or dashed line indicates the hydrogen bond. The most frequent donor and acceptor atoms are the second-row elements nitrogen (N), oxygen (O), and fluorine (F). Hydrogen bonds can be intermolecular (occurring between separate molecules) or intramolecular (occurring among parts of the same molecule). The energy of a hydrogen bond depends on the geometry, the environment, and the nature of the specific donor and acceptor atoms and can vary between 1 and 40 kcal/mol. This makes them somewhat stronger than a van der Waals interaction, and weaker than fully covalent o ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Native Contact
In protein folding, a native contact is a contact between the side chains of two amino acids that are not neighboring in the amino acid sequence (i.e., they are more than four residues apart in the primary sequence in order to remove trivial i to i+4 contacts along alpha helices) but are spatially close in the protein's native state tertiary structure. The fraction of native contacts reproduced in a particular structure is often used as a reaction coordinate for measuring the deviation from the native state of structures produced during molecular dynamics simulations or in benchmarks of 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 differen ... methods. The contact order is a measure of the locality of a protein's native contacts; that is, the sequence distanc ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Secondary Structure
Protein secondary structure is the three dimensional form of ''local segments'' of proteins. The two most common secondary structural elements are alpha helices and beta sheets, though beta turns and omega loops occur as well. Secondary structure elements typically spontaneously form as an intermediate before the protein folds into its three dimensional tertiary structure. Secondary structure is formally defined by the pattern of hydrogen bonds between the amino hydrogen and carboxyl oxygen atoms in the peptide backbone. Secondary structure may alternatively be defined based on the regular pattern of backbone dihedral angles in a particular region of the Ramachandran plot regardless of whether it has the correct hydrogen bonds. The concept of secondary structure was first introduced by Kaj Ulrik Linderstrøm-Lang at Stanford in 1952. Other types of biopolymers such as nucleic acids also possess characteristic secondary structures. Types The most common seconda ... [...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 relat ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Plane (geometry)
In mathematics, a plane is a Euclidean ( flat), two-dimensional surface that extends indefinitely. A plane is the two-dimensional analogue of a point (zero dimensions), a line (one dimension) and three-dimensional space. Planes can arise as subspaces of some higher-dimensional space, as with one of a room's walls, infinitely extended, or they may enjoy an independent existence in their own right, as in the setting of two-dimensional Euclidean geometry. Sometimes the word ''plane'' is used more generally to describe a two-dimensional surface, for example the hyperbolic plane and elliptic plane. When working exclusively in two-dimensional Euclidean space, the definite article is used, so ''the'' plane refers to the whole space. Many fundamental tasks in mathematics, geometry, trigonometry, graph theory, and graphing are performed in a two-dimensional space, often in the plane. Euclidean geometry Euclid set forth the first great landmark of mathematical thought, an axio ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Alpha Carbon
In the nomenclature of organic chemistry, a locant is a term to indicate the position of a functional group or substituent within a molecule. Numeric locants The International Union of Pure and Applied Chemistry (IUPAC) recommends the use of numeric prefixes to indicate the position of substituents, generally by identifying the parent hydrocarbon chain and assigning the carbon atoms based on their substituents in order of precedence. For example, there are at least two isomers of the linear form of pentanone, a ketone that contains a chain of exactly five carbon atoms. There is an oxygen atom bonded to one of the middle three carbons (if it were bonded to an end carbon, the molecule would be an aldehyde, not a ketone), but it is not clear where it is located. In this example, the carbon atoms are numbered from one to five, which starts at one end and proceeds sequentially along the chain. Now the position of the oxygen atom can be defined as on carbon atom number tw ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Peptide Bond
In organic chemistry, a peptide bond is an amide type of covalent chemical bond linking two consecutive alpha-amino acids from C1 (carbon number one) of one alpha-amino acid and N2 (nitrogen number two) of another, along a peptide or protein chain. It can also be called a eupeptide bond to distinguish it from an isopeptide bond, which is another type of amide bond between two amino acids. Synthesis When two amino acids form a ''dipeptide'' through a ''peptide bond'', it is a type of condensation reaction. In this kind of condensation, two amino acids approach each other, with the non- side chain (C1) carboxylic acid moiety of one coming near the non-side chain (N2) amino moiety of the other. One loses a hydrogen and oxygen from its carboxyl group (COOH) and the other loses a hydrogen from its amino group (NH2). This reaction produces a molecule of water (H2O) and two amino acids joined by a peptide bond (−CO−NH−). The two joined amino acids are called a dipeptide. The ... [...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] |
CASP
Critical Assessment of Structure Prediction (CASP), sometimes called Critical Assessment of Protein Structure Prediction, is a community-wide, worldwide experiment for protein structure prediction taking place every two years since 1994. CASP provides research groups with an opportunity to objectively test their structure prediction methods and delivers an independent assessment of the state of the art in protein structure modeling to the research community and software users. Even though the primary goal of CASP is to help advance the methods of identifying protein three-dimensional structure from its amino acid sequence many view the experiment more as a “world championship” in this field of science. More than 100 research groups from all over the world participate in CASP on a regular basis and it is not uncommon for entire groups to suspend their other research for months while they focus on getting their servers ready for the experiment and on performing the detailed predic ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
