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Protein 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] [Amazon] |
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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] [Amazon] |
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Root Mean Square
In mathematics, the root mean square (abbrev. RMS, or rms) of a set of values is the square root of the set's mean square. Given a set x_i, its RMS is denoted as either x_\mathrm or \mathrm_x. The RMS is also known as the quadratic mean (denoted M_2), a special case of the generalized mean. The RMS of a continuous function is denoted f_\mathrm and can be defined in terms of an integral of the square of the function. In estimation theory, the root-mean-square deviation of an estimator measures how far the estimator strays from 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 the square of the function that defines the continuous waveform. In the case of a set of ''n'' values \, the RMS is : x_\text = \sqrt. The corresponding formula for a continuous function (or waveform) ''f''(''t'') defined over the interval T_1 \le t \le T_2 is : f_\text = \sqrt , and the R ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
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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. The algebra of quaternions is often denoted by (for ''Hamilton''), or in blackboard bold by \mathbb H. Quaternions are not a field, because multiplication of quaternions is not, in general, commutative. Quaternions provide a definition of the quotient of two vectors in a three-dimensional space. Quaternions are generally represented in the form a + b\,\mathbf i + c\,\mathbf j +d\,\mathbf k, where the coefficients , , , are real numbers, and , are the ''basis vectors'' or ''basis elements''. 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, robotics, magnetic resonance i ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
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Hydrogen Bond
In chemistry, a hydrogen bond (H-bond) is a specific type of molecular interaction that exhibits partial covalent character and cannot be described as a purely electrostatic force. It occurs when a hydrogen (H) atom, Covalent bond, covalently bonded to a more Electronegativity, electronegative donor atom or group (Dn), interacts with another electronegative atom bearing a lone pair of electrons—the hydrogen bond acceptor (Ac). Unlike simple Dipole–dipole attraction, dipole–dipole interactions, hydrogen bonding arises from charge transfer (nB → σ*AH), Atomic orbital, orbital interactions, and quantum mechanical Delocalized electron, delocalization, making it a resonance-assisted interaction rather than a mere electrostatic attraction. The general notation for hydrogen bonding is Dn−H···Ac, where the solid line represents a polar covalent bond, and the dotted or dashed line indicates the hydrogen bond. The most frequent donor and acceptor atoms are nitrogen (N), oxyg ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
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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 methods. The contact order is a measure of the locality of a protein's native contacts; that is, the sequence distance between amino acids that form contacts. Proteins with low contact order are thought to fold faster and some may be candidates for downhill folding Downhill folding is a process in which a protein folds without encountering any significant macroscopic ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
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Secondary Structure
Protein secondary structure is the local spatial conformation of the polypeptide backbone excluding the side chains. The two most common Protein structure#Secondary structure, secondary structural elements are alpha helix, 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 protein folding, folds into its three dimensional protein tertiary structure, tertiary structure. Secondary structure is formally defined by the pattern of hydrogen bonds between the Amine, amino hydrogen and carboxyl oxygen atoms in the peptide backbone chain, backbone. Secondary structure may alternatively be defined based on the regular pattern of backbone Dihedral angle#Dihedral angles of proteins, 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 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
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Rotamer
In chemistry, rotamers are chemical species that differ from one another primarily due to rotations about one or more single bonds. Various arrangements of atoms in a molecule that differ by rotation about single bonds can also be referred to as conformations. Conformers/rotamers differ little in their energies, so they are almost never separable in a practical sense. Rotations about single bonds are subject to small energy barriers. When the time scale for interconversion is long enough for isolation of individual rotamers (usually arbitrarily defined as a half-life of interconversion of 1000 seconds or longer), the species are termed atropisomers (''see:'' atropisomerism). The ring-flip of substituted cyclohexanes constitutes a common form of conformers. The study of the energetics of bond rotation is referred to as conformational analysis. In some cases, conformational analysis can be used to predict and explain product selectivity, mechanisms, and rates of reactions. Conform ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
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Plane (geometry)
In mathematics, a Euclidean plane is a Euclidean space of dimension two, denoted \textbf^2 or \mathbb^2. It is a geometric space in which two real numbers are required to determine the position of each point. It is an affine space, which includes in particular the concept of parallel lines. It has also metrical properties induced by a distance, which allows to define circles, and angle measurement. A Euclidean plane with a chosen Cartesian coordinate system is called a '' Cartesian plane''. The set \mathbb^2 of the ordered pairs of real numbers (the real coordinate plane), equipped with the dot product, is often called ''the'' Euclidean plane or ''standard Euclidean plane'', since every Euclidean plane is isomorphic to it. History Books I through IV and VI of Euclid's Elements dealt with two-dimensional geometry, developing such notions as similarity of shapes, the Pythagorean theorem (Proposition 47), equality of angles and areas, parallelism, the sum of the angles ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
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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 two, three o ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
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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] [Amazon] |
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Side Chain
In organic chemistry and biochemistry, a side chain is a substituent, chemical group that is attached to a core part of the molecule called the "main chain" or backbone chain, 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 structural formulae. 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 "r ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |
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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 predictio ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] [Amazon] |