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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] |
Ramachandran Plot Original Outlines
The Tamil and Malayali name Ramachandran may refer to: * A. Ramachandran (born 1935), an Indian painter * A. Ramachandran (politician) the incumbent mayor of Salem, Tamil Nadu * C. R. Ramachandran, an Indian politician * G. Ramachandran (1904–1995), an Indian social reformer and politician * Gopalasamudram Narayana Iyer Ramachandran (1922–2001), an Indian biophysicist known for creating the Ramachandran plot * K. V. Ramachandran (1898–1956), an Indian music and art critic * M. Ramachandran, an Indian politician * M. D. R. Ramachandran (1934–2024), an Indian politician * M. G. Ramachandran, also known as MGR (1917–1987), an Indian film actor and former Chief Minister of Tamil Nadu * N. S. Ramachandran (born 1908 (?)), an Indian composer of Carnatic music * P. P. Ramachandran, an Indian poet * R. Ramachandran, an Indian poet * Subramaniam Ramachandran, a missing Sri Lankan journalist * T. Ramachandran (CPI politician), an Indian politician * T. Ramachandran (INC p ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
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, which is overseen by the Worldwide Protein Data Bank (wwPDB). This structural data is obtained and deposited by biologists and biochemists worldwide through the use of experimental methodologies such as X-ray crystallography, Nuclear magnetic resonance spectroscopy of proteins, NMR spectroscopy, and, increasingly, cryo-electron microscopy. All submitted data are reviewed by expert Biocuration, biocurators and, once approved, are made freely available on the Internet under the CC0 Public Domain Dedication. Global access to the data is provided by the websites of the wwPDB member organizations (PDBe, PDBj, RCSB PDB, and BMRB). The PDB is a key in areas of structural biology, such as structural genomics. Most major scientific journals and some funding agencies now require scientists to submit their structure data to the PDB. Many other ... [...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). 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] |
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 English interrogative word * "What?", one of the Five Ws used in journalism Film and television * ''What!'' (film), also known as ''The Whip and the Body'', a 1963 Italian film directed by Mario Bava * ''What?'' (film), a 1972 film directed by Roman Polanski * " What?!", a 2019 episode of the TV series ''Barry'' * "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 specializing in punk and indie music * 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 ''Looki ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Visual Molecular Dynamics
Visual Molecular Dynamics (VMD) is a molecular modelling and Visualization (computer graphics), 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 (software), RenderMan, Tachyon (software), Tachyon, Virtual Reality Modeling Language (VRML), and many others. Users can run their own Tcl and Python (programming language), 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 th ... [...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] |
STING
Stimulator of interferon genes (STING), also known as transmembrane protein 173 (TMEM173) and MPYS/MITA/ERIS is a regulator protein that in humans is encoded by the STING1 gene. STING plays an important role in innate immunity. STING induces type I interferon production when cells are infected with intracellular pathogens, such as viruses, mycobacteria and intracellular parasites. Type I interferon, mediated by STING, protects infected cells and nearby cells from local infection by binding to the same cell that secretes it (autocrine signaling) and nearby cells (paracrine signaling.) It thus plays an important role, for instance, in controlling norovirus infection. STING works as both a direct cytosolic DNA sensor (CDS) and an adaptor protein in Type I interferon signaling through different molecular mechanisms. It has been shown to activate downstream transcription factors STAT6 and IRF3 through TBK1, which are responsible for antiviral response and innate immune response aga ... [...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 hemicellulose 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] |
Laurence A
Laurence is in modern use as an English masculine and a French feminine given name. The modern English masculine name is a variant of Lawrence and originates from a French form of the Latin ''Laurentius'', a name meaning "man from Laurentum". The French feminine name Laurence is derived from the same source and is used in French-speaking countries as a form of the masculine ''Laurent''. The name was used in the Middle Ages for both males and females in honor of Saint Laurence, one of the seven deacons of Rome. In England, it was also given in reference to Saint Laurence of Canterbury. In other languages: Lorenzo (Italian, Spanish), Lorenz (German). In Ireland, Laurence has traditionally been used as an Anglicization of the Irish masculine name Lorcan or Lorcán. Usage Laurence, used as a spelling variant of the more popular Lawrence, was in regular use for boys in the Anglosphere since the medieval era. It was most popular for boys in English-speaking countries during the ... [...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 ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
