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Root Mean Square Deviation (bioinformatics)
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 proteins. Note that RMSD calculation can be applied to other, non-protein molecules, such as small organic 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 wid ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Bioinformatics
Bioinformatics () is an interdisciplinary field that develops methods and software tools for understanding biological data, in particular when the data sets are large and complex. As an interdisciplinary field of science, bioinformatics combines biology, chemistry, physics, computer science, information engineering, mathematics and statistics to analyze and interpret the biological data. Bioinformatics has been used for '' in silico'' analyses of biological queries using computational and statistical techniques. Bioinformatics includes biological studies that use computer programming as part of their methodology, as well as specific analysis "pipelines" that are repeatedly used, particularly in the field of genomics. Common uses of bioinformatics include the identification of candidates genes and single nucleotide polymorphisms (SNPs). Often, such identification is made with the aim to better understand the genetic basis of disease, unique adaptations, desirable properties (e ... [...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 ''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 of lig ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Statistical Deviation And Dispersion
Statistics (from German: '' Statistik'', "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.Dodge, Y. (2006) ''The Oxford Dictionary of Statistical Terms'', Oxford University Press. When census data 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 exp ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Python (programming Language)
Python is a high-level, general-purpose programming language. Its design philosophy emphasizes code readability with the use of significant indentation. Python is dynamically-typed and garbage-collected. It supports multiple programming paradigms, including structured (particularly 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 and first released it in 1991 as Python 0.9.0. Python 2.0 was released in 2000 and introduced new features such as list comprehensions, cycle-detecting garbage collection, reference counting, and Unicode support. Python 3.0, released in 2008, was a major revision that is not completely backward-compatible with earlier versions. Python 2 was discontinued with version 2.7.18 in 2020. Python consistently ranks as ... [...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 * Local government, a form of public administration, usually the lowest tier of administration * Local news, coverage of events in a local context which would not normally be of interest to those of other localities * Local union, a locally based trade union organization which forms part of a larger union 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 * Local TV LLC, an American television broadcasting company * Locast, a non-profit streaming service offering local, over-the-air television * ''The Local'' (film), a 2008 action-drama film * '' The Local'', English-language news websites in several European countries Computing * .local, a network address component * Local variable, a variable that is given loc ... [...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 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, rangin ... [...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 * Long, Washington, United States People * Long (surname) * Long (surname 龍) (Chinese surname) Fictional characters * Long (''Bloody Roar''), in the video game series 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 Shanghai * ... [...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 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, rangin ... [...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 them ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Root Mean Square Fluctuation
In statistical mechanics, the mean squared displacement (MSD, also 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 Mean Squared Displacement 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, which is twice the square root of MSD), is also used in studying the transportation and mixing phenomena in the realm of environmental engineering. It prominently appears in the Debye–Waller factor (describing vibrations within the solid state) and in the Langevin equation (describi ... [...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 a frequently used measure of the differences between values (sample or population values) predicted by a model or an estimator and the values observed. The RMSD represents the square root of the second sample moment of the differences between predicted values and observed values or the quadratic mean of these differences. These deviations are called '' residuals'' when the calculations are performed over the data sample that was used for estimation and are called ''errors'' (or prediction errors) when computed out-of-sample. The RMSD serves to aggregate the magnitudes of the errors in predictions for various data points into a single measure of predictive power. RMSD is a measure of accuracy, to compare forecasting errors of different models for a particular dataset and not between datasets, as it is scale-dependent. RMSD is always non-negative, and a value of 0 (almost never achieved in practice) would ind ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
