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Ribbon Diagram
Ribbon diagrams, also known as Richardson diagrams, are three-dimensional space, 3D schematic representations of protein structure and are one of the most common methods of protein depiction used today. The ribbon depicts the general course and organization of the protein backbone in 3D and serves as a visual framework for hanging details of the entire atomic structure, such as the balls for the oxygen atoms attached to myoglobin's active site in the adjacent figure. Ribbon diagrams are generated by interpolating a smooth curve through the polypeptide backbone. Alpha helix, α-helices are shown as coiled ribbons or thick tubes, Beta sheet, β-sheets as arrows, and non-repetitive coils or loops as lines or thin tubes. The direction of the Peptide, polypeptide chain is shown locally by the arrows, and may be indicated overall by a colour ramp along the length of the ribbon. Ribbon diagrams are simple yet powerful, expressing the visual basics of a molecular structure (twist, fold an ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Myoglobin
Myoglobin (symbol Mb or MB) is an iron- and oxygen-binding protein found in the cardiac and skeletal muscle, skeletal Muscle, muscle tissue of vertebrates in general and in almost all mammals. Myoglobin is distantly related to hemoglobin. Compared to hemoglobin, myoglobin has a higher affinity for oxygen and does not have cooperative binding with oxygen like hemoglobin does. Myoglobin consists of non-polar amino acids at the core of the globulin, where the heme group is non-covalently bounded with the surrounding polypeptide of myoglobin. In humans, myoglobin is found in the bloodstream only after Strain (injury), muscle injury. (Google books link is the 2008 edition) High concentrations of myoglobin in muscle cells allow organisms to hold their breath for a longer period of time. Diving mammals such as whales and seals have muscles with particularly high abundance of myoglobin. Myoglobin is found in Type I muscle, Type II A, and Type II B; although many older texts describe myo ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Hermite Spline
In the mathematics, mathematical subfield of numerical analysis, a Hermite spline is a spline curve where each polynomial of the spline is in Hermite polynomials, Hermite form. See also *Cubic Hermite spline *Hermite polynomials *Hermite interpolation References {{mathapplied-stub Splines (mathematics) Interpolation ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Graphics
Molecular graphics is the discipline and philosophy of studying molecules and their properties through graphical representation. IUPAC limits the definition to representations on a "graphical display device". Ever since Dalton's atoms and Kekulé's benzene, there has been a rich history of hand-drawn atoms and molecules, and these representations have had an important influence on modern molecular graphics. Colour molecular graphics are often used on chemistry journal covers artistically. History Prior to the use of computer graphics in representing molecular structure, Robert Corey and Linus Pauling developed a system for representing atoms or groups of atoms from hard wood on a scale of 1 inch = 1 angstrom connected by a clamping device to maintain the molecular configuration. These early models also established the CPK coloring scheme that is still used today to differentiate the different types of atoms in molecular models (e.g. carbon = black, oxygen = red, nitrogen ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ball-and-stick Model
In chemistry, the ball-and-stick model is a molecular model of a chemical substance which displays both the Molecular geometry, three-dimensional position of the atoms and the chemical bond, bonds between them. The atoms are typically represented by sphere (geometry), spheres, connected by rods which represent the bonds. Double bond, Double and triple bonds are usually represented by two or three curved rods, respectively, or alternately by correctly positioned sticks for the sigma bond, sigma and pi bonds. In a good model, the angles between the rods should be the same as the Bond angle, angles between the bonds, and the distances between the centers of the spheres should be proportional to the distances between the corresponding atomic nucleus, atomic nuclei. The chemical element of each atom is often indicated by the sphere's color. In a ball-and-stick model, the radius of the spheres is usually much smaller than the rod lengths, in order to provide a clearer view of the atoms ... [...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] |
Warren DeLano
Warren Lyford DeLano (June 21, 1972 – November 3, 2009) was a bioinformatician and an advocate for the increased adoption of open source practices in the sciences, and especially drug discovery, where advances which save time and resources can also potentially save lives. Biography Born in Philadelphia on June 21, 1972, DeLano was educated at Yale University, where he helped produce campus humor magazine ''The Yale Record''. In 2000, he launched the PyMOL open-source molecular viewer in an attempt to demonstrate the practical impact open source might have on discovery of new medicines. Since then, PyMOL has been widely adopted for molecular structure visualization within the pharmaceutical industry and at public sector research institutions. In 2003, DeLano founded DeLano Scientific LLC to commercialize PyMOL and conduct an experiment in the "laboratory of the market" regarding the commercial viability of an open source software company. His hypothesis was that open source so ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
PyMOL
PyMOL is a source-available molecular visualization system created by Warren Lyford DeLano. It was commercialized initially by DeLano Scientific LLC, which was a private software company dedicated to creating useful tools that become universally accessible to scientific and educational communities. It is currently commercialized by Schrödinger, Inc. As the original software license was a permissive licence, they were able to remove it; new versions are no longer released under the Python license, but under a custom license (granting broad use, redistribution, and modification rights, but assigning copyright to any version to Schrödinger, LLC.), and some of the source code is no longer released. PyMOL can produce high-quality 3D images of small molecules and biological macromolecules, such as proteins. PyMOL is widely used. PyMOL is one of the few mostly open-source model visualization tools available for use in structural biology. The ''Py'' part of the software's name refe ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Electron Microscopy
An electron microscope is a microscope that uses a beam of electrons as a source of illumination. It uses electron optics that are analogous to the glass lenses of an optical light microscope to control the electron beam, for instance focusing it to produce magnified images or electron diffraction patterns. As the wavelength of an electron can be up to 100,000 times smaller than that of visible light, electron microscopes have a much higher resolution of about 0.1 nm, which compares to about 200 nm for light microscopes. ''Electron microscope'' may refer to: * Transmission electron microscope (TEM) where swift electrons go through a thin sample * Scanning transmission electron microscope (STEM) which is similar to TEM with a scanned electron probe * Scanning electron microscope (SEM) which is similar to STEM, but with thick samples * Electron microprobe similar to a SEM, but more for chemical analysis * Low-energy electron microscope (LEEM), used to image surfaces * ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Scientific Visualization
Scientific visualization ( also spelled scientific visualisation) is an interdisciplinary branch of science concerned with the visualization of scientific phenomena. Michael Friendly (2008)"Milestones in the history of thematic cartography, statistical graphics, and data visualization" It is also considered a subset of computer graphics, a branch of computer science. The purpose of scientific visualization is to graphically illustrate scientific data to enable scientists to understand, illustrate, and glean insight from their data. Research into how people read and misread various types of visualizations is helping to determine what types and features of visualizations are most understandable and effective in conveying information. History One of the earliest examples of three-dimensional scientific visualisation was Maxwell's thermodynamic surface, sculpted in clay in 1874 by James Clerk Maxwell. This prefigured modern scientific visualization techniques that use computer gr ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
UCSF Chimera
UCSF Chimera (or simply Chimera) is an extensible program for interactive visualization and analysis of molecular structures and related data, including density maps, supramolecular assemblies, sequence alignments, docking results, trajectories, and conformational ensembles. High-quality images and movies can be created. Chimera includes complete documentation and can be downloaded free of charge for noncommercial use. Chimera is developed by the Resource for Biocomputing, Visualization, and Informatics (RBVI) at the University of California, San Francisco. Development is partially supported by the National Institutes of Health (NIGMS grant P41-GM103311). Chimera is no longer actively developed and is superseded by UCSF ChimeraX. General structure analysis * automatic identification of atom * hydrogen addition and partial charge assignment * high-quality hydrogen bond, contact, and clash detection * measurements: distances, angles, surface area, volume * calculation of cent ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Jmol
Jmol is computer software for molecular modelling of chemical structures in 3 dimensions. It is an open-source Java viewer for chemical structures in 3D. The name originated from ''Jva (the programming language) + olcules, and also the mol file format. JSmol is an implementation in JavaScript of the functionality of Jmol. It can hence be embedded in web pages to display interactive 3D models of molecules and other structures without the need for any software apart from the web browser (''it does not use Java''). Both Jmol and JSmol render an interactive 3D representation of a molecule or other structure that may be used as a teaching tool, or for research, in several fields, e.g. chemistry, biochemistry, materials science, crystallography, symmetry or nanotechnology. Software Jmol is written in the programming language Java, so it can run on different operating systems: Windows, macOS, Linux, and Unix, as long as they have Java installed. It is free and open-source so ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
