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X-PLOR
X-PLOR is a computer software package for computational structural biology originally developed by Axel T. Brunger at Yale University. It was first published in 1987 as an offshoot of CHARMM - a similar program that ran on supercomputers made by Cray Inc. It is used in the fields of X-ray crystallography and nuclear magnetic resonance spectroscopy of proteins (NMR) analysis. X-PLOR is a highly sophisticated program that provides an interface between theoretical foundations and experimental data in structural biology, with specific emphasis on X-ray crystallography and nuclear magnetic resonance spectroscopy in solution of biological macro-molecules. It is intended mainly for researchers and students in the fields of computational chemistry, structural biology, and computational molecular biology. See also *Comparison of software for molecular mechanics modeling *Molecular mechanics Molecular mechanics uses classical mechanics to model molecular systems. The Born–Oppenheimer ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
CHARMM
Chemistry at Harvard Macromolecular Mechanics (CHARMM) is the name of a widely used set of force fields for molecular dynamics, and the name for the molecular dynamics simulation and analysis computer software package associated with them. The CHARMM Development Project involves a worldwide network of developers working with Martin Karplus and his group at Harvard to develop and maintain the CHARMM program. Licenses for this software are available, for a fee, to people and groups working in academia. Force fields The CHARMM force fields for proteins include: united-atom (sometimes termed ''extended atom'') CHARMM19, all-atom CHARMM22 and its dihedral potential corrected variant CHARMM22/CMAP, as well as later versions CHARMM27 and CHARMM36 and various modifications such as CHARMM36m and CHARMM36IDPSFF. In the CHARMM22 protein force field, the atomic partial charges were derived from quantum chemical calculations of the interactions between model compounds and water. Furthermor ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Molecular Mechanics
Molecular mechanics uses classical mechanics to model molecular systems. The Born–Oppenheimer approximation is assumed valid and the potential energy of all systems is calculated as a function of the nuclear coordinates using Force field (chemistry), force fields. Molecular mechanics can be used to study molecule systems ranging in size and complexity from small to large biological systems or material assemblies with many thousands to millions of atoms. All-atomistic molecular mechanics methods have the following properties: * Each atom is simulated as one particle * Each particle is assigned a radius (typically the van der Waals radius), polarizability, and a constant net charge (generally derived from quantum calculations and/or experiment) * Bonded interactions are treated as ''springs'' with an equilibrium distance equal to the experimental or calculated bond length Variants on this theme are possible. For example, many simulations have historically used a ''united-atom'' ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Software
Software consists of computer programs that instruct the Execution (computing), execution of a computer. Software also includes design documents and specifications. The history of software is closely tied to the development of digital computers in the mid-20th century. Early programs were written in the machine language specific to the hardware. The introduction of high-level programming languages in 1958 allowed for more human-readable instructions, making software development easier and more portable across different computer architectures. Software in a programming language is run through a compiler or Interpreter (computing), interpreter to execution (computing), execute on the architecture's hardware. Over time, software has become complex, owing to developments in Computer network, networking, operating systems, and databases. Software can generally be categorized into two main types: # operating systems, which manage hardware resources and provide services for applicat ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Axel T
Axel may refer to: People * Axel (name), all persons with the name Places * Axel, Netherlands, a town ** Capture of Axel, a battle at Axel in 1586 Arts, entertainment, media * ''Axel'', a 1988 short film by Nigel Wingrove * ''Axel'', a Cirque du Soleil show * ''Axël'', an 1890 drama play by Auguste Villiers de l'Isle-Adam * Axel (dance turn), a type of turn performed in dance * Axel lift, a movement in pair skating * Axel jump, a type of jump in figure skating * "Axel F", the 1985 instrumental theme song of ''Beverly Hills Cop'' by Harold Faltermeyer Companies, organizations * Axel Hotels, hotel chain * Axel Springer SE, largest digital publishing house in Europe Other uses * Axel Maersk, Danish container ship * Citroën Axel, automobile made by Citroën * Typhoon Axel (other), multiple storms named Axel * Axel, a character in Pikwik Pack * Axel, a coaxial two-wheeler, designed to investigate caves on the moon with the proposed mission Moon Diver (spacecraft) S ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Yale University
Yale University is a Private university, private Ivy League research university in New Haven, Connecticut, United States. Founded in 1701, Yale is the List of Colonial Colleges, third-oldest institution of higher education in the United States, and one of the nine colonial colleges chartered before the American Revolution. Yale was established as the Collegiate School in 1701 by Congregationalism in the United States, Congregationalist clergy of the Connecticut Colony. Originally restricted to instructing ministers in theology and sacred languages, the school's curriculum expanded, incorporating humanities and sciences by the time of the American Revolution. In the 19th century, the college expanded into graduate and professional instruction, awarding the first Doctor of Philosophy, PhD in the United States in 1861 and organizing as a university in 1887. Yale's faculty and student populations grew rapidly after 1890 due to the expansion of the physical campus and its scientif ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Supercomputer
A supercomputer is a type of computer with a high level of performance as compared to a general-purpose computer. The performance of a supercomputer is commonly measured in floating-point operations per second (FLOPS) instead of million instructions per second (MIPS). Since 2022, supercomputers have existed which can perform over 1018 FLOPS, so called Exascale computing, exascale supercomputers. For comparison, a desktop computer has performance in the range of hundreds of gigaFLOPS (1011) to tens of teraFLOPS (1013). Since November 2017, all of the TOP500, world's fastest 500 supercomputers run on Linux-based operating systems. Additional research is being conducted in the United States, the European Union, Taiwan, Japan, and China to build faster, more powerful and technologically superior exascale supercomputers. Supercomputers play an important role in the field of computational science, and are used for a wide range of computationally intensive tasks in various fields, ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Cray
Cray Inc., a subsidiary of Hewlett Packard Enterprise, is an American supercomputer manufacturer headquartered in Seattle, Washington. It also manufactures systems for data storage and analytics. Several Cray supercomputer systems are listed in the TOP500, which ranks the most powerful supercomputers in the world. In 1972, the company was founded by computer designer Seymour Cray as Cray Research, Inc., and it continues to manufacture parts in Chippewa Falls, Wisconsin, where Cray was born and raised. After being acquired by Silicon Graphics in 1996, the modern company was formed after being purchased in 2000 by Tera Computer Company, which adopted the name Cray Inc. In 2019, the company was acquired by Hewlett Packard Enterprise for $1.3 billion. History Background: 1950–1972 In 1950, Seymour Cray began working in the computing field when he joined Engineering Research Associates (ERA) in Saint Paul, Minnesota. There, he helped to create the ERA 1103. ERA eventually ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
X-ray Crystallography
X-ray crystallography is the experimental science of determining the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to Diffraction, diffract in specific directions. By measuring the angles and intensities of the X-ray diffraction, a crystallography, crystallographer can produce a three-dimensional picture of the density of electrons within the crystal and the positions of the atoms, as well as their chemical bonds, crystallographic disorder, and other information. X-ray crystallography has been fundamental in the development of many scientific fields. In its first decades of use, this method determined the size of atoms, the lengths and types of chemical bonds, and the atomic-scale differences between various materials, especially minerals and alloys. The method has also revealed the structure and function of many biological molecules, including vitamins, drugs, proteins and nucleic acids such as DNA. X-ray crystall ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Nuclear Magnetic Resonance Spectroscopy Of Proteins
Nuclear magnetic resonance spectroscopy of proteins (usually abbreviated protein NMR) is a field of structural biology in which NMR spectroscopy is used to obtain information about the structure and dynamics of proteins, and also nucleic acids, and their complexes. The field was pioneered by Richard R. Ernst and Kurt Wüthrich at the ETH, and by Ad Bax, Marius Clore, Angela Gronenborn at the NIH, and Gerhard Wagner at Harvard University, among others. Structure determination by NMR spectroscopy usually consists of several phases, each using a separate set of highly specialized techniques. The sample is prepared, measurements are made, interpretive approaches are applied, and a structure is calculated and validated. NMR involves the quantum-mechanical properties of the central core (" nucleus") of the atom. These properties depend on the local molecular environment, and their measurement provides a map of how the atoms are linked chemically, how close they are in space, and how ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
