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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 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] |
Ramachandran Plot Original Outlines
The Tamil and Malayali name Ramachandran may refer to: * A. Ramachandran (born 1935), Indian painter * C. R. Ramachandran, politician * G. Ramachandran (1904–1995), Indian social reformer, and politician * Gopalasamudram Narayana Iyer Ramachandran (1922–2001), biophysicist who created the Ramachandran Map * K. V. Ramachandran (1898–1956), Indian music and art critic * M. Ramachandran, politician * M. G. Ramachandran, also known as MGR, (1917–1987), Tamil film actor and former Chief Minister of Tamil Nadu * N. S. Ramachandran (born 1908 (?)), Carnatic music composer * P. P. Ramachandran, Malayalam poet * R. Ramachandran, Malayalam poet * Subramaniam Ramachandran, missing Sri Lankan Tamil Journalist * T. Ramachandran (1944–2000), Malayalam author * T. Ramachandran (politician), Indian politician * T. A. Ramachandran (1912–1951), Indian cricket umpire * T. K. Ramachandran (died 1993), Indian film actor and producer in Tamil cinema * T. N. Ramachandran (1903–1973), ar ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Crystallography
Crystallography is the experimental science of determining the arrangement of atoms in crystalline solids. Crystallography is a fundamental subject in the fields of materials science and solid-state physics (condensed matter physics). The word "crystallography" is derived from the Greek word κρύσταλλος (''krystallos'') "clear ice, rock-crystal", with its meaning extending to all solids with some degree of transparency, and γράφειν (''graphein'') "to write". In July 2012, the United Nations recognised the importance of the science of crystallography by proclaiming that 2014 would be the International Year of Crystallography. denote a direction vector (in real space). * Coordinates in ''angle brackets'' or ''chevrons'' such as <100> denote a ''family'' of directions which are related by symmetry operations. In the cubic crystal system for example, would mean 00 10 01/nowiki> or the negative of any of those directions. * Miller indices in ''parentheses'' ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Sirius Visualization Software
Sirius is a molecular modelling and analysis system developed at San Diego Supercomputer Center. Sirius is designed to support advanced user requirements that go beyond simple display of small molecules and proteins. Sirius supports high quality interactive 3D graphics, structure building, displaying protein or DNA primary sequences, access to remote data sources, and visualizing molecular dynamics trajectories. It can be used for scientific visualization and analysis, and chemistry and biology instruction. This software is no longer supported as of 2011. Key features Sirius supports a variety of applications with a set of features, including: * Building and editing chemical structures using a library of fragments * Protein structure and sequence alignment * Command line interpreter and scripting support fully compatible with extant RasMol scripts * Full support for molecular dynamics trajectory visualizing * BLAST search directly in Protein Data Bank and Uniprot databases * A ... [...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). The next-generation program is 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 centroids, axes, planes and associate ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
WHAT IF Software
WHAT IF is a computer program used in a wide variety of computational (''in silico'') macromolecular structure research fields. The software provides a flexible environment to display, manipulate, and analyze small and large molecules, proteins, nucleic acids, and their interactions. History The first version of the WHAT IF software was developed by Gert Vriend in 1987 at the University of Groningen, Groningen, Netherlands. Most of its development occurred during 1989–2000 at the European Molecular Biology Laboratory (EMBL) in Heidelberg, Germany. Other contributors include Chris Sander, and Wolfgang Kabsch. In 2000, maintenance of the software moved to the Dutch Center for Molecular and Biomolecular Informatics (CMBI) in Nijmegen, Netherlands. It is available for in-house use, or as a web-based resource. , the original paper describing WHAT IF has been cited more than 4,000 times. Software WHAT IF provides a flexible environment to display, manipulate, and analyze small mole ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
WHAT CHECK
What or WHAT may refer to: * What, an interrogative pronoun and adverb * "What?", one of the Five Ws used in journalism Film and television * ''What!'' (film) or ''The Whip and the Body'', a 1963 Italian film directed by Mario Bava * '' What?'' (film), a 1972 film directed by Roman Polanski * "What", the name of the second baseman in Abbott and Costello's comedy routine "Who's on First?" * "What?", the catchphrase of professional wrestler Stone Cold Steve Austin Music * ''what.'', a comedy/music album by Bo Burnham, 2013 * What Records, a UK record label * What? Records, a US record label Songs * "What" (song), by Melinda Marx, 1965 * "What?" (Rob Zombie song), 2009 * "What?" (SB19 song), 2021 * "What?", by 666 from ''The Soft Boys'' * "What", by Bassnectar from ''Vava Voom'' * "What?", by Corrosion of Conformity from '' Eye for an Eye'' * "What?", by the Move from ''Looking On'' * "What?", by A Tribe Called Quest from ''The Low-End Theory'' Science and technology * Web ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Visual Molecular Dynamics
Visual Molecular Dynamics (VMD) is a molecular modelling and visualization computer program. VMD is developed mainly as a tool to view and analyze the results of molecular dynamics simulations. It also includes tools for working with volumetric data, sequence data, and arbitrary graphics objects. Molecular scenes can be exported to external rendering tools such as POV-Ray, RenderMan, Tachyon, Virtual Reality Modeling Language (VRML), and many others. Users can run their own Tcl and Python scripts within VMD as it includes embedded Tcl and Python interpreters. VMD runs on Unix, Apple Mac macOS, and Microsoft Windows. VMD is available to non-commercial users under a distribution-specific license which permits both use of the program and modification of its source code, at no charge. History VMD has been developed under the aegis of principal investigator Klaus Schulten in the Theoretical and Computational Biophysics group at the Beckman Institute for Advanced Science and Technolog ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Pymol
PyMOL is an open source but proprietary 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 Schrodinger, 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. According to the original author, by 2009, almost a quarter of all published images of 3D protein structures in the scientific literature were made using PyMOL. PyMOL ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
STING
Sting may refer to: * Stinger or sting, a structure of an animal to inject venom, or the injury produced by a stinger * Irritating hairs or prickles of a stinging plant, or the plant itself Fictional characters and entities * Sting (Middle-earth), a fictional sword in J. R. R. Tolkien's ''The Hobbit'' and ''The Lord of the Rings'' * Sting Oakley, a character in ''Gundam Seed Destiny'' * Peter Stanchek (comics), a character nicknamed "Sting" in the Valiant Comics universe * Trixie Sting, a character in the TV series ''Slugterra'' * Kamen Rider Sting, a character in the TV series '' Kamen Rider Dragon Knight'' Music * ''Sting'' (EP), 2016, by Stellar * "Sting" (Eric Saade song), 2015 * "Sting" (Fletcher song), 2022 * Sting (musical phrase), a short sequence of music used in films and TV as a form of punctuation * Sting (percussion), a brief burst of percussion to punctuate a joke * "Sting" (Stellar song), 2016 People * Sting (musician) (born 1951), English musician and acto ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Polysaccharide
Polysaccharides (), or polycarbohydrates, are the most abundant carbohydrates found in food. They are long chain polymeric carbohydrates composed of monosaccharide units bound together by glycosidic linkages. This carbohydrate can react with water (hydrolysis) using amylase enzymes as catalyst, which produces constituent sugars (monosaccharides, or oligosaccharides). They range in structure from linear to highly branched. Examples include storage polysaccharides such as starch, glycogen and galactogen and structural polysaccharides such as cellulose and chitin. Polysaccharides are often quite heterogeneous, containing slight modifications of the repeating unit. Depending on the structure, these macromolecules can have distinct properties from their monosaccharide building blocks. They may be amorphous or even insoluble in water. When all the monosaccharides in a polysaccharide are the same type, the polysaccharide is called a homopolysaccharide or homoglycan, but when more t ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Biophysics
Molecular biophysics is a rapidly evolving interdisciplinary area of research that combines concepts in physics, chemistry, engineering, mathematics and biology. It seeks to understand biomolecular systems and explain biological function in terms of molecular structure, structural organization, and dynamic behaviour at various levels of complexity (from single molecules to supramolecular structures, viruses and small living systems). This discipline covers topics such as the measurement of molecular forces, molecular associations, allosteric interactions, Brownian motion, and cable theory. Additional areas of study can be found on Outline of Biophysics. The discipline has required development of specialized equipment and procedures capable of imaging and manipulating minute living structures, as well as novel experimental approaches. Overview Molecular biophysics typically addresses biological questions similar to those in biochemistry and molecular biology, seeking to find the ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Beta Sheet
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 versi ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
