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Coot (software)
The program Coot (Crystallographic Object-Oriented Toolkit) is used to display and manipulate atomic models of macromolecules, typically of proteins or nucleic acids, using 3D computer graphics. It is primarily focused on building and validation of atomic models into three-dimensional electron density maps obtained by X-ray crystallography methods, although it has also been applied to data from electron microscopy. Overview Coot displays electron density maps and atomic models and allows model manipulations such as idealization, real space refinement, manual rotation/translation, rigid-body fitting, ligand search, solvation, mutations, rotamers, and Ramachandran idealization. The software is designed to be easy-to-learn for novice users, achieved by ensuring that tools for common tasks are 'discoverable' through familiar user interface elements (menus and toolbars), or by intuitive behaviour (mouse controls). Recent developments have enhanced the usability of the software for exp ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Paul Emsley (crystallographer)
Paul Emsley is a British crystallographer at the MRC Laboratory of Molecular Biology in Cambridge. He works as an independent scientist and is a member of the Computational Crystallography Group headed by Garib Murshudov. Emsley is the primary author of the model-building software Coot,Emsley, P., Lohkamp, B., Scott, W.G. and Cowtan, K., 2010Features and development of Coot ''Acta Crystallographica Section D'', ''66''(4), pp.486-501. a tool for building models of proteins whose three dimensional structures are determined via X-ray crystallography or cryo-EM. These protein structures are deposited at the Worldwide Protein Data Bank for collaboration among scientists. Since its introduction in 2004, Coot has remained as free software Free software or libre software is computer software distributed under terms that allow users to run the software for any purpose as well as to study, change, and distribute it and any adapted versions. Free software is a matter of liberty, no .. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
University Of California At Santa Cruz
The University of California, Santa Cruz (UC Santa Cruz or UCSC) is a public land-grant research university in Santa Cruz, California. It is one of the ten campuses in the University of California system. Located on Monterey Bay, on the edge of the coastal community of Santa Cruz, the campus lies on of rolling, forested hills overlooking the Pacific Ocean. Founded in 1965, UC Santa Cruz began with the intention to showcase progressive, cross-disciplinary undergraduate education, innovative teaching methods and contemporary architecture. The residential college system consists of ten small colleges that were established as a variation of the Oxbridge collegiate university system. Among the Faculty is 1 Nobel Prize Laureate, 1 Breakthrough Prize in Life Sciences recipient, 12 members from the National Academy of Sciences, 28 members of the American Academy of Arts and Sciences, and 40 members of the American Association for the Advancement of Science. Eight UC Santa Cruz alumni ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Gerard Kleywegt
Gerard Jacob Kleywegt (born 5 June 1962, in Rozenburg) is a Dutch X-ray crystallographer and the former team leader of the Protein Data Bank in Europe at the EBI; a member of the Worldwide Protein Data Bank. Education Kleywegt obtained his PhD from the University of Utrecht in 1991. Career After his PhD, Kleywegt did postdoctoral research with Alwyn Jones at Uppsala University. before moving to the EBI. Research Kleywegt's research focuses on protein crystallography and the Protein Data Bank The Protein Data Bank (PDB) is a database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The data, typically obtained by X-ray crystallography, NMR spectroscopy, or, increasingly, cry .... References {{DEFAULTSORT:Kleywegt, Gerard 1962 births Living people Dutch biochemists Crystallographers Leiden University alumni Utrecht University alumni People from Rozenburg ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Torsion Angle
A dihedral angle is the angle between two intersecting planes or half-planes. In chemistry, it is the clockwise angle between half-planes through two sets of three atoms, having two atoms in common. In solid geometry, it is defined as the union of a line and two half-planes that have this line as a common edge. In higher dimensions, a dihedral angle represents the angle between two hyperplanes. The planes of a flying machine are said to be at positive dihedral angle when both starboard and port main planes (commonly called wings) are upwardly inclined to the lateral axis. When downwardly inclined they are said to be at a negative dihedral angle. Mathematical background When the two intersecting planes are described in terms of Cartesian coordinates by the two equations : a_1 x + b_1 y + c_1 z + d_1 = 0 :a_2 x + b_2 y + c_2 z + d_2 = 0 the dihedral angle, \varphi between them is given by: :\cos \varphi = \frac and satisfies 0\le \varphi \le \pi/2. Alternatively, if and ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Beta Strand
The beta sheet, (β-sheet) (also β-pleated sheet) is a common motif of the regular protein secondary structure. Beta sheets consist of beta strands (β-strands) connected laterally by at least two or three backbone hydrogen bonds, forming a generally twisted, pleated sheet. A β-strand is a stretch of polypeptide chain typically 3 to 10 amino acids long with backbone in an extended conformation. The supramolecular association of β-sheets has been implicated in the formation of the fibrils and protein aggregates observed in amyloidosis, notably Alzheimer's disease. History The first β-sheet structure was proposed by William Astbury in the 1930s. He proposed the idea of hydrogen bonding between the peptide bonds of parallel or antiparallel extended β-strands. However, Astbury did not have the necessary data on the bond geometry of the amino acids in order to build accurate models, especially since he did not then know that the peptide bond was planar. A refined version was p ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Alpha Helix
The alpha helix (α-helix) is a common motif in the secondary structure of proteins and is a right hand-helix conformation in which every backbone N−H group hydrogen bonds to the backbone C=O group of the amino acid located four residues earlier along the protein sequence. The alpha helix is also called a classic Pauling–Corey–Branson α-helix. The name 3.613-helix is also used for this type of helix, denoting the average number of residues per helical turn, with 13 atoms being involved in the ring formed by the hydrogen bond. Among types of local structure in proteins, the α-helix is the most extreme and the most predictable from sequence, as well as the most prevalent. Discovery In the early 1930s, William Astbury showed that there were drastic changes in the X-ray fiber diffraction of moist wool or hair fibers upon significant stretching. The data suggested that the unstretched fibers had a coiled molecular structure with a characteristic repeat of ≈. Astb ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Crystallography And NMR System
CNS or Crystallography and NMR system, is a software library for computational structural biology. It is an offshoot of X-PLOR and uses much of the same syntax. It is used in the fields of X-ray crystallography and NMR spectroscopy Nuclear magnetic resonance spectroscopy, most commonly known as NMR spectroscopy or magnetic resonance spectroscopy (MRS), is a spectroscopic technique to observe local magnetic fields around atomic nuclei. The sample is placed in a magnetic fiel ... of biological macromolecules. References {{Reflist External linksThe program's webpage and reference manual Science software Computer libraries ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
CCP4 (file Format)
The CCP4 file format is file generated by the Collaborative Computational Project Number 4 in 1979. The file format for electron density has become industry standard in X-ray crystallography and Cryo-electron microscopy where the result of the technique is a three-dimensional grid of voxels each with a value corresponding to density of electrons (see wave function) The CCP4 format is supported by almost every molecular graphics suite that supports volumetric data. The major packages include: *Visual molecular dynamics *PyMOL *UCSF Chimera *Bsoft *Coot *MOE See also *MTZ (file format) *MRC (file format) * EZD (file format) *Chemical file format **Protein Data Bank (file format) *Voxel In 3D computer graphics, a voxel represents a value on a regular grid in three-dimensional space. As with pixels in a 2D bitmap, voxels themselves do not typically have their position (i.e. coordinates) explicitly encoded with their values. Ins ... - one way of presenting 3D densities Externa ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
