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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] |
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 biological organisms, minerals and 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 network featuring many-to-many links, or a lattice featuring connections between components that are neighbors in space. Load-bearing Buildings, aircraft, skeletons, anthills, beaver dams, bridges and salt domes are all examples of load-bearing structures. The results of construction are divided into buildings and non-building structures, and make up the infrastructure of a human society. Built structures are broadly divided by their varying design approaches and standards, into categories including building structures, archi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Rutgers
Rutgers University (; RU), officially Rutgers, The State University of New Jersey, is a public land-grant research university consisting of four 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 the nine U.S. 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 but it has evolved into a coeducational public research university after being design ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Random Coil Index
Random coil index (RCI) predicts protein flexibility by calculating an inverse weighted average of backbone secondary chemical shifts and predicting values of model-free order parameters as well as per-residue RMSD of NMR and molecular dynamics ensembles from this parameter. The key advantages of this protocol over existing methods of studying protein flexibility are # it does not require prior knowledge of a protein's tertiary structure, # it is not sensitive to the protein's overall tumbling and # it does not require additional NMR measurements beyond the standard experiments for backbone assignments. The application of secondary chemical shifts to characterize protein flexibility is based on an assumption that the proximity of chemical shifts to random coil values is a manifestation of increased protein mobility, while significant differences from random coil values are an indication of a relatively rigid structure. Even though chemical shifts of rigid residues may adopt ran ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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] |
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 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", by Camp Mulla * "Low", by Coldplay from '' X&Y'' * "Low", by Inna from the self-titled album * "Low", by Marianas Trench from ''Fix Me'' * "Low", by R.E.M. from '' Out of Time'' * "Low", by Silverchair from ''Young Modern'' * "Low", by Sleeping with Sirens from ''Feel'' * "Low", by Tech N9ne from ''K.O.D.'' * ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Electron Density
In quantum chemistry, 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 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 th ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Anisotropy
Anisotropy () is the property of a material which allows it to change or assume different properties in different directions, as opposed to isotropy. It can be defined as a difference, when measured along different axes, in a material's physical or mechanical properties (absorbance, refractive index, conductivity, tensile strength, etc.). An example of anisotropy is light coming through a polarizer. Another is wood, which is easier to split along its grain than across it. 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 steeply angled with respect to the point of view. Older techniques, such as bilinear and trilinear filtering, do not take into account the angle a surface is viewed from, which can result in aliasing or bl ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Complementarity Plot
The complementarity plot (CP) is a graphical tool for structural validation of atomic models for both folded globular proteins and 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 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 inter-protein complexes. The software is included in the bioi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 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 RNA polymerase transcribes DNA in ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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 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 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 Ramachandran plot "wrap" right-to-left and bottom-to-top. For ins ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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