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Root Mean Square Deviation Of Atomic Positions
In bioinformatics, the root mean square deviation of atomic positions, or simply root mean square deviation (RMSD), is the measure of the average distance between the atoms (usually the backbone atoms) of superimposed molecules. In the study of globular protein conformations, one customarily measures the similarity in three-dimensional structure by the RMSD of the Cα atomic coordinates after optimal rigid body superposition. When a dynamical system fluctuates about some well-defined average position, the RMSD from the average over time can be referred to as the ''RMSF'' or root mean square fluctuation. The size of this fluctuation can be measured, for example using Mössbauer spectroscopy or nuclear magnetic resonance, and can provide important physical information. The Lindemann index is a method of placing the RMSF in the context of the parameters of the system. A widely used way to compare the structures of biomolecules or solid bodies is to translate and rotate one structure ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bioinformatics
Bioinformatics () is an interdisciplinary field of science that develops methods and Bioinformatics software, software tools for understanding biological data, especially when the data sets are large and complex. Bioinformatics uses biology, chemistry, physics, computer science, data science, computer programming, information engineering, mathematics and statistics to analyze and interpret biological data. The process of analyzing and interpreting data can sometimes be referred to as computational biology, however this distinction between the two terms is often disputed. To some, the term ''computational biology'' refers to building and using models of biological systems. Computational, statistical, and computer programming techniques have been used for In silico, computer simulation analyses of biological queries. They include reused specific analysis "pipelines", particularly in the field of genomics, such as by the identification of genes and single nucleotide polymorphis ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ligand (biochemistry)
In biochemistry and pharmacology, a ligand is a substance that forms a complex with a biomolecule to serve a biological purpose. The etymology stems from Latin ''ligare'', which means 'to bind'. In protein-ligand binding, the ligand is usually a molecule which produces a signal by binding to a site on a target protein. The binding typically results in a change of conformational isomerism (conformation) of the target protein. In DNA-ligand binding studies, the ligand can be a small molecule, ion, or protein which binds to the DNA double helix. The relationship between ligand and binding partner is a function of charge, hydrophobicity, and molecular structure. Binding occurs by intermolecular forces, such as ionic bonds, hydrogen bonds and Van der Waals forces. The association or docking is actually reversible through dissociation. Measurably irreversible covalent bonding between a ligand and target molecule is atypical in biological systems. In contrast to the definition o ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Statistical Deviation And Dispersion
Statistics (from German: ', "description of a state, a country") is the discipline that concerns the collection, organization, analysis, interpretation, and presentation of data. In applying statistics to a scientific, industrial, or social problem, it is conventional to begin with a statistical population or a statistical model to be studied. Populations can be diverse groups of people or objects such as "all people living in a country" or "every atom composing a crystal". Statistics deals with every aspect of data, including the planning of data collection in terms of the design of surveys and experiments. When census data (comprising every member of the target population) cannot be collected, statisticians collect data by developing specific experiment designs and survey samples. Representative sampling assures that inferences and conclusions can reasonably extend from the sample to the population as a whole. An experimental study involves taking measurements of the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Python (programming Language)
Python is a high-level programming language, high-level, general-purpose programming language. Its design philosophy emphasizes code readability with the use of significant indentation. Python is type system#DYNAMIC, dynamically type-checked and garbage collection (computer science), garbage-collected. It supports multiple programming paradigms, including structured programming, structured (particularly procedural programming, procedural), object-oriented and functional programming. It is often described as a "batteries included" language due to its comprehensive standard library. Guido van Rossum began working on Python in the late 1980s as a successor to the ABC (programming language), ABC programming language, and he first released it in 1991 as Python 0.9.0. Python 2.0 was released in 2000. Python 3.0, released in 2008, was a major revision not completely backward-compatible with earlier versions. Python 2.7.18, released in 2020, was the last release of ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Local Global Alignment
Local may refer to: Geography and transportation * Local (train), a train serving local traffic demand * Local, Missouri, a community in the United States Arts, entertainment, and media * ''Local'' (comics), a limited series comic book by Brian Wood and Ryan Kelly * ''Local'' (novel), a 2001 novel by Jaideep Varma * ''The Local'' (film), a 2008 action-drama film * ''The Local'', English-language news websites in several European countries Computing * .local, a network address component Mathematics * Local property, a property which occurs on ''sufficiently small'' or ''arbitrarily small'' neighborhoods of points * Local ring, type of ring in commutative algebra Other uses * Pub, a drinking establishment, known as a "local" to its regulars See also * * * Local group (other) * Locale (other) * Localism (other) * Locality (other) * Localization (other) * Locus (other) * Lokal (other) Lokal may refer to: ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Global Distance Calculation
The global distance test (GDT), also written as GDT_TS to represent "total score", is a measure of similarity between two protein structures with known amino acid correspondences (e.g. identical amino acid sequences) but different tertiary structures. It is most commonly used to compare the results of protein structure prediction to the experimentally determined structure as measured by X-ray crystallography, protein NMR, or, increasingly, cryoelectron microscopy. The GDT metric was developed by Adam Zemla at Lawrence Livermore National Laboratory and originally implemented in the Local-Global Alignment (LGA) program. It is intended as a more accurate measurement than the common root-mean-square deviation (RMSD) metric - which is sensitive to outlier regions created, for example, by poor modeling of individual loop regions in a structure that is otherwise reasonably accurate. The conventional GDT_TS score is computed over the alpha carbon atoms and is reported as a percentage, r ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Longest Continuous Segment
Long may refer to: Measurement * Long, characteristic of something of great duration * Long, characteristic of something of great length * Longitude (abbreviation: long.), a geographic coordinate * Longa (music), note value in early music mensural notation Places Asia * Long District, Laos * Long District, Phrae, Thailand * Longjiang (other) or River Long (lit. "dragon river"), one of several rivers in China * Yangtze River or Changjiang (lit. "Long River"), China Elsewhere * Long, Somme, France People * Long (Chinese surname) * Long (Western surname) Fictional characters * Long (''Bloody Roar''), in the video game series * Long, Aeon of Permanence in Honkai: Star Rail Sports * Long, a fielding term in cricket * Long, in tennis and similar games, beyond the service line during a serve and beyond the baseline during play Other uses * , a U.S. Navy ship name * Long (finance), a position in finance, especially stock markets * Lòng, name for a laneway in Shan ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Template Modeling Score
In bioinformatics, the template modeling score or TM-score is a measure of similarity between two protein structures. The TM-score is intended as a more accurate measure of the global similarity of full-length protein structures than the often used RMSD measure. The TM-score indicates the similarity between two structures by a score between (0,1], where 1 indicates a perfect match between two structures (thus the higher the better). Generally scores below 0.20 corresponds to randomly chosen unrelated proteins whereas structures with a score higher than 0.5 assume roughly the same fold. A quantitative study shows that proteins of TM-score = 0.5 have a posterior probability of 37% in the same CATH topology family and of 13% in the same SCOP fold family. The probabilities increase rapidly when TM-score > 0.5. The TM-score is designed to be independent of protein lengths. The TM-score equation TM-score between two protein structures (e.g., a template structure and a target st ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Global Distance Test
The global distance test (GDT), also written as GDT_TS to represent "total score", is a measure of similarity between two protein structures with known amino acid correspondences (e.g. identical amino acid sequences) but different tertiary structures. It is most commonly used to compare the results of protein structure prediction to the experimentally determined structure as measured by X-ray crystallography, protein NMR, or, increasingly, cryoelectron microscopy. The GDT metric was developed by Adam Zemla at Lawrence Livermore National Laboratory and originally implemented in the Local-Global Alignment (LGA) program. It is intended as a more accurate measurement than the common root-mean-square deviation (RMSD) metric - which is sensitive to outlier regions created, for example, by poor modeling of individual loop regions in a structure that is otherwise reasonably accurate. The conventional GDT_TS score is computed over the alpha carbon atoms and is reported as a percentage, r ... [...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. 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] |
Root Mean Square Fluctuation
In statistical mechanics, the mean squared displacement (MSD), also called mean square displacement, average squared displacement, or mean square fluctuation, is a measure of the deviation of the position of a particle with respect to a reference position over time. It is the most common measure of the spatial extent of random motion, and can be thought of as measuring the portion of the system "explored" by the random walker. In the realm of biophysics and environmental engineering, the MSD is measured over time to determine if a particle is spreading slowly due to diffusion, or if an advective force is also contributing. Another relevant concept, the variance-related diameter (VRD), defined as twice the square root of MSD, is also used in studying the transportation and mixing phenomena in environmental engineering. It prominently appears in the Debye–Waller factor (describing vibrations within the solid state) and in the Langevin equation (describing diffusion of a Brown ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Root Mean Square Deviation
The root mean square deviation (RMSD) or root mean square error (RMSE) is either one of two closely related and frequently used measures of the differences between true or predicted values on the one hand and observed values or an estimator on the other. The deviation is typically simply a differences of scalars; it can also be generalized to the vector lengths of a displacement, as in the bioinformatics concept of root mean square deviation of atomic positions. RMSD of a sample The RMSD of a sample is the quadratic mean of the differences between the observed values and predicted ones. These deviations are called '' residuals'' when the calculations are performed over the data sample that was used for estimation (and are therefore always in reference to an estimate) and are called ''errors'' (or prediction errors) when computed out-of-sample (aka on the full set, referencing a true value rather than an estimate). The RMSD serves to aggregate the magnitudes of the errors in ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
