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Structure Validation
Macromolecular structure validation is the process of evaluating reliability for 3-dimensional atomic models of large biological molecules such as proteins and nucleic acids. These models, which provide 3D coordinates for each atom in the molecule (see example in the image), come from structural biology experiments such as x-ray crystallography or nuclear magnetic resonance (NMR). The validation has three aspects: 1) checking on the validity of the thousands to millions of measurements in the experiment; 2) checking how consistent the atomic model is with those experimental data; and 3) checking consistency of the model with known physical and chemical properties. Proteins and nucleic acids are the workhorses of biology, providing the necessary chemical reactions, structural organization, growth, mobility, reproduction, and environmental sensitivity. Essential to their biological functions are the detailed 3D structures of the molecules and the changes in those structures. To und ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Structure Validation Concept
A structure is an arrangement and organization of interrelated elements in a material object or system, or the object or system so organized. Material structures include man-made objects such as buildings and machines and natural objects such as organism, biological organisms, minerals and chemical substance, chemicals. Abstract structures include data structures in computer science and musical form. Types of structure include a hierarchy (a cascade of one-to-many relationships), a Complex network, network featuring many-to-many Link (geometry), links, or a lattice (order), lattice featuring connections between components that are neighbors in space. Load-bearing Buildings, aircraft, skeletons, Ant colony, anthills, beaver dams, bridges and salt domes are all examples of Structural load, load-bearing structures. The results of construction are divided into buildings and nonbuilding structure, non-building structures, and make up the infrastructure of a human society. Built str ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Rutgers
Rutgers University ( ), officially Rutgers, The State University of New Jersey, is a public land-grant research university consisting of three campuses in New Jersey. Chartered in 1766, Rutgers was originally called Queen's College and was affiliated with the Dutch Reformed Church. It is the eighth-oldest college in the United States, the second-oldest in New Jersey (after Princeton University), and one of nine colonial colleges that were chartered before the American Revolution.Stoeckel, Althea"Presidents, professors, and politics: the colonial colleges and the American revolution", ''Conspectus of History'' (1976) 1(3):45–56. In 1825, Queen's College was renamed Rutgers College in honor of Colonel Henry Rutgers, whose substantial gift to the school had stabilized its finances during a period of uncertainty. For most of its existence, Rutgers was a private liberal arts college. It has evolved into a coeducational public research university since being designated the Stat ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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PROSESS
Protein Structure Evaluation Suite & Server (PROSESS) is a freely available web server for protein structure validation. It has been designed at the University of Alberta to assist with the process of evaluating and validating protein structures solved by NMR spectroscopy. Structure validation Structure validation is a particularly important component of the structure determination pipeline as many protein structures have small structural errors (i.e. distorted bond lengths or angles, incompatible torsion angles, overlapping atoms) that are not easily detected by visual inspection. For protein structures solved by NMR spectroscopy, where large numbers of structures are generated and where coordinate inaccuracies are common, this problem is particularly acute. Methodology Most NMR-based structure validation protocols primarily use NOE ( Nuclear Overhauser Enhancement), J-coupling or residual dipolar coupling ( RDC ) data to assess or validate structures. In particular, they ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Low Vs High Resolution Hemoglobin Detail
Low or LOW or lows, may refer to: People * Low (surname), listing people surnamed Low Places * Low, Quebec, Canada * Low, Utah, United States * Lo Wu station (MTR code LOW), Hong Kong; a rail station * Salzburg Airport (ICAO airport code: LOWS), Austria Music * Low (band), an American indie rock group from Duluth, Minnesota * Low (English band), an English duo featuring Frankie Goes to Hollywood guitarist Brian Nash Albums * ''Low'' (David Bowie album), 1977 * ''Low'' (Testament album), 1994 * ''Low'' (Low EP), 1994 Songs * "Low" (Cracker song), 1993 * "Low" (Flo Rida song), 2007 * "Low" (Foo Fighters song), 2002 * "Low" (Juicy J song), 2014 * "Low" (Kelly Clarkson song), 2003 * "Low" (Lenny Kravitz song), 2018 * "Low" (Sara Evans song), 2008 * "Low" (SZA song), 2022 * "Low", by Camp Mulla * "Low", by Coldplay from the 2005 album '' X&Y'' * "Low", by I Prevail from the 2019 album '' Trauma'' * "Low", by Inna from her 2015 self-titled album * "Low", by Marianas ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Electron Density
Electron density or electronic density is the measure of the probability of an electron being present at an infinitesimal element of space surrounding any given point. It is a scalar quantity depending upon three spatial variables and is typically denoted as either \rho(\textbf r) or n(\textbf r). The density is determined, through definition, by the normalised N-electron wavefunction which itself depends upon 4N variables (3N spatial and N Spin (physics), spin coordinates). Conversely, the density determines the wave function modulo up to a phase factor, providing the formal foundation of density functional theory. According to quantum mechanics, due to the uncertainty principle on an atomic scale the exact location of an electron cannot be predicted, only the probability of its being at a given position; therefore electrons in atoms and molecules act as if they are "smeared out" in space. For one-electron systems, the electron density at any point is proportional to the square ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Anisotropy
Anisotropy () is the structural property of non-uniformity in different directions, as opposed to isotropy. An anisotropic object or pattern has properties that differ according to direction of measurement. For example, many materials exhibit very different physical or mechanical properties when measured along different axes, e.g. absorbance, refractive index, conductivity, and tensile strength. An example of anisotropy is light coming through a polarizer. Another is wood, which is easier to split along its grain than across it because of the directional non-uniformity of the grain (the grain is the same in one direction, not all directions). Fields of interest Computer graphics In the field of computer graphics, an anisotropic surface changes in appearance as it rotates about its geometric normal, as is the case with velvet. Anisotropic filtering (AF) is a method of enhancing the image quality of textures on surfaces that are far away and viewed at a shallow angle. Older ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Collaborative Computational Project Number 4
The Collaborative Computational Project Number 4 in protein crystallography, Protein Crystallography (CCP4) was set up in 1979 in the United Kingdom to support collaboration between researchers working in software development and assemble a comprehensive collection of software for structural biology. The CCP4 core team is located at the Research Complex at Harwell (RCaH) at Rutherford Appleton Laboratory (RAL) in Didcot, near Oxford, UK. CCP4 was originally supported by the UK Science and Engineering Research Council (SERC), and is now supported by the Biotechnology and Biological Sciences Research Council (BBSRC). The project is coordinated at Daresbury Laboratory, CCLRC Daresbury Laboratory. The results of this effort gave rise to the CCP4 program suite,M.D. Winn, C.C. Ballard, K.D. Cowtan, E.J. Dodson, P. Emsley, P.R. Evans, R.M. Keegan, E.B. Krissinel, A.G.W. Leslie, A. McCoy, S.J. McNicholas, G.N. Murshudov, N.S. Pannu, E.A. Potterton, H.R. Powell, R.J. Read, A. Vagin, K.S. W ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Complementarity Plot
The complementarity plot (CP) is a graphical tool for structural validation of atomic models for both folded Globular protein, globular proteins and Protein-protein interface, protein-protein interfaces.Basu S, Bhattacharyya D, Banerjee R (2012) Self-Complementarity within Proteins: Bridging the Gap between Binding and Folding. Biophys J 102:2605–2614 . doi: 10.1016/j.bpj.2012.04.029 http://www.saha.ac.in/biop/www/sarama.htmlBasu S, Bhattacharyya D, Banerjee R (2014) Applications of complementarity plot in error detection and structure validation of proteins. Indian J Biochem Biophys 51:188–200 It is based on a probabilistic representation of preferred amino acid side-chain orientation, analogous to the preferred backbone orientation of Ramachandran plot, Ramachandran plots). It can potentially serve to elucidate protein folding as well as binding. The upgraded versions of the software suite is available and maintained in ''github'' for both folded globular proteins as well as ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Base Pair
A base pair (bp) is a fundamental unit of double-stranded nucleic acids consisting of two nucleobases bound to each other by hydrogen bonds. They form the building blocks of the DNA double helix and contribute to the folded structure of both DNA and RNA. Dictated by specific hydrogen bonding patterns, "Watson–Crick" (or "Watson–Crick–Franklin") base pairs (guanine–cytosine and adenine–thymine) allow the DNA helix to maintain a regular helical structure that is subtly dependent on its nucleotide sequence. The Complementarity (molecular biology), complementary nature of this based-paired structure provides a Redundancy (information theory), redundant copy of the genetic information encoded within each strand of DNA. The regular structure and data redundancy provided by the DNA double helix make DNA well suited to the storage of genetic information, while base-pairing between DNA and incoming nucleotides provides the mechanism through which DNA polymerase replicates DNA and ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Backbone-dependent Rotamer Library
In biochemistry, a backbone-dependent rotamer library provides the frequencies, mean dihedral angles, and standard deviations of the discrete conformations (known as rotamers) of the amino acid Side_chain#Biochemistry, side chains in proteins as a function of the protein backbone, backbone dihedral angles φ and ψ of the Ramachandran plot, Ramachandran map. By contrast, backbone-independent rotamer libraries express the frequencies and mean dihedral angles for all side chains in proteins, regardless of the backbone conformation of each residue type. Backbone-dependent rotamer libraries have been shown to have significant advantages over backbone-independent rotamer libraries, principally when used as an energy term, by speeding up search times of side-chain packing algorithms used in protein structure prediction and protein design. History The first backbone-dependent rotamer library was developed in 1993 by Roland Dunbrack and Martin Karplus to assist the prediction of the Carte ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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Ramachandran Plot
In biochemistry, a Ramachandran plot (also known as a Rama plot, a Ramachandran diagram or a �,ψplot), originally developed in 1963 by G. N. Ramachandran, C. Ramakrishnan, and V. Sasisekharan, is a way to visualize energetically allowed regions for backbone dihedral angles (also called as torsional angles, phi and psi angles) ψ against φ of amino acid residues in protein structure. The figure on the left illustrates the definition of the φ and ψ backbone dihedral angles (called φ and φ' by Ramachandran). The ω angle at the peptide bond is normally 180°, since the partial-double-bond character keeps the peptide bond planar. The figure in the top right shows the allowed φ,ψ backbone conformational regions from the Ramachandran et al. 1963 and 1968 hard-sphere calculations: full radius in solid outline, reduced radius in dashed, and relaxed tau (N-Cα-C) angle in dotted lines. Because dihedral angle values are circular and 0° is the same as 360°, the edges of the R ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |