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Protein Data Bank
The Protein
Protein
Data Bank (PDB) is a crystallographic 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, cryo-electron microscopy, and submitted by biologists and biochemists from around the world, are freely accessible on the Internet via the websites of its member organisations (PDBe,[1] PDBj,[2] and RCSB[3]). The PDB is overseen by an organization called the Worldwide Protein
Protein
Data Bank, wwPDB. The PDB is a key resource 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
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Coordinated Universal Time
Coordinated Universal Time
Universal Time
(abbreviated to UTC) is the primary time standard by which the world regulates clocks and time. It is within about 1 second of mean solar time at 0° longitude,[1] and is not adjusted for daylight saving time
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Protein Structure Prediction
Protein
Protein
structure prediction is the inference of the three-dimensional structure of a protein from its amino acid sequence—that is, the prediction of its folding and its secondary and tertiary structure from its primary structure. Structure prediction is fundamentally different from the inverse problem of protein design. Protein structure prediction is one of the most important goals pursued by bioinformatics and theoretical chemistry; it is highly important in medicine (for example, in drug design) and biotechnology (for example, in the design of novel enzymes). Every two years, the performance of current methods is assessed in the CASP
CASP
experiment (Critical Assessment of Techniques for Protein
Protein
Structure Prediction)
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Visual Molecular Dynamics
Visual molecular dynamics (VMD) is a molecular modelling and visualization computer program.[2] VMD is developed as mainly 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
Tcl
and Python scripts within VMD as it includes embedded Tcl
Tcl
and Python interpreters
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Weizmann Institute Of Science
The Weizmann Institute of Science
Weizmann Institute of Science
(Hebrew: מכון ויצמן למדע‎ Machon Weizmann LeMada) is a public research university in Rehovot, Israel, established in 1934, 14 years before the State of Israel. It differs from other Israeli universities in that it offers only graduate and postgraduate degrees in the natural and exact sciences. It is a multidisciplinary research center, with around 3,800 scientists, postdoctoral fellows, Ph.D. and M.Sc
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Structure Factor
In condensed matter physics and crystallography, the static structure factor (or structure factor for short) is a mathematical description of how a material scatters incident radiation. The structure factor is a critical tool in the interpretation of scattering patterns (interference patterns) obtained in X-ray, electron and neutron diffraction experiments. Confusingly, there are two different mathematical expressions in use, both called 'structure factor'. One is usually written S ( q ) displaystyle S(mathbf q ) ; it is more generally valid, and relates the observed diffracted intensity per atom to that produced by a single scattering unit. The other is usually written F displaystyle F or F h k l displaystyle F_ hkl and is only valid for systems with long-range positional order — crystals
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Texas A&M University
A university (Latin: universitas, "a whole") is an institution of higher (or tertiary) education and research which awards academic degrees in various academic disciplines
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Brookhaven National Laboratory
Brookhaven National Laboratory
Brookhaven National Laboratory
(BNL) is a United States Department of Energy national laboratory located in Upton, New York, on Long Island, and was formally established in 1947 at the site of Camp Upton, a former U.S. Army base. Its name stems from its location within the Town of Brookhaven, approximately 60 miles east of New York City. Research at BNL specializes in nuclear and high energy physics, energy science and technology, environmental and bioscience, nanoscience and national security. The 5300 acre campus contains several large research facilities, including the Relativistic Heavy Ion Collider
Relativistic Heavy Ion Collider
and National Synchrotron Light Source
National Synchrotron Light Source
II. Seven Nobel prizes have been awarded for work conducted at Brookhaven lab
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Distance Geometry
The distance geometry problem is that of characterization and study of sets of points based only on given values of the distances between member pairs.[1][2][3] Therefore distance geometry has immediate relevance where distance values are determined or considered, such as biology,[4] sensor network,[5] surveying, cartography, and physics.Contents1 Applications 2 Basic issues 3 Cayley–Menger determinants 4 Discretization and orders 5 Software for distance geometry 6 Books and conferences 7 See also 8 ReferencesApplications[edit] The distance geometry problem (DGP) is that of finding the coordinates of a set of points by using the distances between some pairs of such points.[3] There exists nowadays a large community that is actively working on this problem, because there are several real-life applications that can lead to the formulation of a DGP
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Discovery Studio
Discovery Studio is a suite of software for simulating small molecule and macromolecule systems
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Chemical Shift
In nuclear magnetic resonance (NMR) spectroscopy, the chemical shift is the resonant frequency of a nucleus relative to a standard in a magnetic field. Often the position and number of chemical shifts are diagnostic of the structure of a molecule.[1][2][3] Chemical shifts are also used to describe signals in other forms of spectroscopy such as photoemission spectroscopy. Some atomic nuclei possess a magnetic moment (nuclear spin), which gives rise to different energy levels and resonance frequencies in a magnetic field. The total magnetic field experienced by a nucleus includes local magnetic fields induced by currents of electrons in the molecular orbitals (note that electrons have a magnetic moment themselves). The electron distribution of the same type of nucleus (e.g. 1H, 13C, 15N) usually varies according to the local geometry (binding partners, bond lengths, angles between bonds, and so on), and with it the local magnetic field at each nucleus
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3DEM
Cryogenic
Cryogenic
transmission electron microscopy (CryoTEM), or transmission electron cryomicroscopy, is a form of cryogenic electron microscopy, more specifically a type of transmission electron microscopy (TEM) where the sample is studied at cryogenic temperatures (generally liquid-nitrogen temperatures).[1] CryoTEM is gaining popularity in structural biology.[2] The utility of cryogenic transmission electron microscopy stems from the fact that it allows the observation of specimens that have not been stained or fixed in any way, showing them in their native environment
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UC San Diego
The University of California, San Diego[a] is a public research university located in the La Jolla
La Jolla
neighborhood of San Diego, California, in the United States.[12] The university occupies 2,141 acres (866 ha) near the coast of the Pacific Ocean with the main campus resting on approximately 1,152 acres (466 ha).[13] Established in 1960 near the pre-existing Scripps Institution of Oceanography, UC
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Digital Object Identifier
In computing, a digital object identifier (DOI) is a persistent identifier or handle used to identify objects uniquely, standardized by the International Organization for Standardization (ISO).[1] An implementation of the Handle System,[2][3] DOIs are in wide use mainly to identify academic, professional, and government information, such as journal articles, research reports and data sets, and official publications though they also have been used to identify other types of information resources, such as commercial videos. A DOI aims to be "resolvable", usually to some form of access to the information object to which the DOI refers. This is achieved by binding the DOI to metadata about the object, such as a URL, indicating where the object can be found. Thus, by being actionable and interoperable, a DOI differs from identifiers such as ISBNs and ISRCs which aim only to identify their referents uniquely
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PubMed Identifier
PubMed
PubMed
is a free search engine accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine
United States National Library of Medicine
(NLM) at the National Institutes of Health
National Institutes of Health
maintains the database as part of the Entrez
Entrez
system of information retrieval.[1] From 1971 to 1997, MEDLINE online access to the MEDLARS Online computerized database primarily had been through institutional facilities, such as university libraries
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PubMed Central
PubMed
PubMed
Central (PMC) is a free digital repository that archives publicly accessible full-text scholarly articles that have been published within the biomedical and life sciences journal literature. As one of the major research databases within the suite of resources that have been developed by the National Center for Biotechnology Information (NCBI), PubMed
PubMed
Central is much more than just a document repository
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