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ResProx
Resolution by Proxy (ResProx) is a method for assessing the equivalent X-ray resolution of NMR-derived protein structures. ResProx calculates resolution from coordinate data rather than from electron density or other experimental inputs. This makes it possible to calculate the resolution of a structure regardless of how it was solved (X-ray, NMR, EM, modeling, ab initio prediction). ResProx was originally designed to serve as a simple, single-number evaluation that allows straightforward comparison between the quality/resolution of X-ray structures and the quality of a given NMR structure. However, it can also be used to assess the reliability of an experimentally reported X-ray structure resolution, to evaluate protein structures solved by unconventional or hybrid means and to identify fraudulent structures deposited in the PDB. ResProx incorporates more than 25 different structural features to determine a single resolution-like value. ResProx values are reported in Angstro ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
David S
David (; , "beloved one") (traditional spelling), , ''Dāwūd''; grc-koi, Δαυΐδ, Dauíd; la, Davidus, David; gez , ዳዊት, ''Dawit''; xcl, Դաւիթ, ''Dawitʿ''; cu, Давíдъ, ''Davidŭ''; possibly meaning "beloved one". was, according to the Hebrew Bible, the third king of the United Kingdom of Israel. In the Books of Samuel, he is described as a young shepherd and harpist who gains fame by slaying Goliath, a champion of the Philistines, in southern Canaan. David becomes a favourite of Saul, the first king of Israel; he also forges a notably close friendship with Jonathan, a son of Saul. However, under the paranoia that David is seeking to usurp the throne, Saul attempts to kill David, forcing the latter to go into hiding and effectively operate as a fugitive for several years. After Saul and Jonathan are both killed in battle against the Philistines, a 30-year-old David is anointed king over all of Israel and Judah. Following his rise to power, David ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
X-ray
An X-ray, or, much less commonly, X-radiation, is a penetrating form of high-energy electromagnetic radiation. Most X-rays have a wavelength ranging from 10 picometers to 10 nanometers, corresponding to frequencies in the range 30 petahertz to 30 exahertz ( to ) and energies in the range 145 eV to 124 keV. X-ray wavelengths are shorter than those of UV rays and typically longer than those of gamma rays. In many languages, X-radiation is referred to as Röntgen radiation, after the German scientist Wilhelm Conrad Röntgen, who discovered it on November 8, 1895. He named it ''X-radiation'' to signify an unknown type of radiation.Novelline, Robert (1997). ''Squire's Fundamentals of Radiology''. Harvard University Press. 5th edition. . Spellings of ''X-ray(s)'' in English include the variants ''x-ray(s)'', ''xray(s)'', and ''X ray(s)''. The most familiar use of X-rays is checking for fractures (broken bones), but X-rays are also used in other ways. ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Coordinate
In geometry, a coordinate system is a system that uses one or more numbers, or coordinates, to uniquely determine the position of the points or other geometric elements on a manifold such as Euclidean space. The order of the coordinates is significant, and they are sometimes identified by their position in an ordered tuple and sometimes by a letter, as in "the ''x''-coordinate". The coordinates are taken to be real numbers in elementary mathematics, but may be complex numbers or elements of a more abstract system such as a commutative ring. The use of a coordinate system allows problems in geometry to be translated into problems about numbers and ''vice versa''; this is the basis of analytic geometry. Common coordinate systems Number line The simplest example of a coordinate system is the identification of points on a line with real numbers using the ''number line''. In this system, an arbitrary point ''O'' (the ''origin'') is chosen on a given line. The coordinate of a po ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Ab Initio Structure Prediction
In computational biology, ''de novo'' protein structure prediction refers to an algorithmic process by which protein tertiary structure is predicted from its amino acid primary sequence. The problem itself has occupied leading scientists for decades while still remaining unsolved. According to Science, the problem remains one of the top 125 outstanding issues in modern science. At present, some of the most successful methods have a reasonable probability of predicting the folds of small, single-domain proteins within 1.5 angstroms over the entire structure. ''De novo'' methods tend to require vast computational resources, and have thus only been carried out for relatively small proteins. De novo protein structure modeling is distinguished from Template-based modeling (TBM) by the fact that no solved homologue to the protein of interest is used, making efforts to predict protein structure from amino acid sequence exceedingly difficult. Prediction of protein structure ''de novo'' for l ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Protein Structure
Protein structure is the three-dimensional arrangement of atoms in an amino acid-chain molecule. Proteins are polymers specifically polypeptides formed from sequences of amino acids, the monomers of the polymer. A single amino acid monomer may also be called a ''residue'' indicating a repeating unit of a polymer. Proteins form by amino acids undergoing condensation reactions, in which the amino acids lose one water molecule per reaction in order to attach to one another with a peptide bond. By convention, a chain under 30 amino acids is often identified as a peptide, rather than a protein. To be able to perform their biological function, proteins fold into one or more specific spatial conformations driven by a number of non-covalent interactions such as hydrogen bonding, ionic interactions, Van der Waals forces, and hydrophobic packing. To understand the functions of proteins at a molecular level, it is often necessary to determine their three-dimensional structure. This is t ... [...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. 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, PDBj, RCSB, and BMRB). The PDB is overseen by an organization called the Worldwide Protein Data Bank, wwPDB. 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 databases use protein structures deposited in the PDB. For example, SCOP and CATH classify protein structures, while PDBsum provides a graphic overview of PDB entries using information from other sources, such as Gene ontology. History Two force ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
X-ray Crystallography
X-ray crystallography is the experimental science determining the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to diffract into many specific directions. By measuring the angles and intensities of these diffracted beams, a crystallographer can produce a three-dimensional picture of the density of electrons within the crystal. From this electron density, the mean positions of the atoms in the crystal can be determined, as well as their chemical bonds, their crystallographic disorder, and various other information. Since many materials can form crystals—such as salts, metals, minerals, semiconductors, as well as various inorganic, organic, and biological molecules—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 among various mat ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Angstrom
The angstromEntry "angstrom" in the Oxford online dictionary. Retrieved on 2019-03-02 from https://en.oxforddictionaries.com/definition/angstrom.Entry "angstrom" in the Merriam-Webster online dictionary. Retrieved on 2019-03-02 from https://www.merriam-webster.com/dictionary/angstrom. (, ; , ) or ångström is a metric unit of length equal to m; that is, one ten-billionth ( US) of a metre, a hundred-millionth of a centimetre,Entry "angstrom" in the Oxford English Dictionary, 2nd edition (1986). Retrieved on 2021-11-22 from https://www.oed.com/oed2/00008552. 0.1 nanometre, or 100 picometres. Its symbol is Å, a letter of the Swedish alphabet. The unit is named after the Swedish physicist Anders Jonas Ångström (1814–1874). The angstrom is often used in the natural sciences and technology to express sizes of atoms, molecules, microscopic biological structures, and lengths of chemical bonds, arrangement of atoms in crystals,Arturas Vailionis (2015):Geometry of Crystals Lect ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Hydrogen Atoms
A hydrogen atom is an atom of the chemical element hydrogen. The Electric charge, electrically neutral atom contains a single positively charged proton and a single negatively charged electron bound to the nucleus by the Coulomb force. Atomic hydrogen constitutes abundance of the chemical elements, about 75% of the baryonic mass of the universe. In everyday life on Earth, isolated hydrogen atoms (called "atomic hydrogen") are extremely rare. Instead, a hydrogen atom tends to combine with other atoms in compounds, or with another hydrogen atom to form ordinary (diatomic) hydrogen gas, H2. "Atomic hydrogen" and "hydrogen atom" in ordinary English use have overlapping, yet distinct, meanings. For example, a water molecule contains two hydrogen atoms, but does not contain atomic hydrogen (which would refer to isolated hydrogen atoms). Atomic spectroscopy shows that there is a discrete infinite set of states in which a hydrogen (or any) atom can exist, contrary to the predictions ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Carbon
Carbon () is a chemical element with the symbol C and atomic number 6. It is nonmetallic and tetravalent In chemistry, the valence (US spelling) or valency (British spelling) of an element is the measure of its combining capacity with other atoms when it forms chemical compounds or molecules. Description The combining capacity, or affinity of an ...—its atom making four electrons available to form covalent bond, covalent chemical bonds. It belongs to group 14 of the periodic table. Carbon makes up only about 0.025 percent of Earth's crust. Three Isotopes of carbon, isotopes occur naturally, Carbon-12, C and Carbon-13, C being stable, while Carbon-14, C is a radionuclide, decaying with a half-life of about 5,730 years. Carbon is one of the Timeline of chemical element discoveries#Ancient discoveries, few elements known since antiquity. Carbon is the 15th Abundance of elements in Earth's crust, most abundant element in the Earth's crust, and the Abundance of the c ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Oxygen
Oxygen is the chemical element with the symbol O and atomic number 8. It is a member of the chalcogen group in the periodic table, a highly reactive nonmetal, and an oxidizing agent that readily forms oxides with most elements as well as with other compounds. Oxygen is Earth's most abundant element, and after hydrogen and helium, it is the third-most abundant element in the universe. At standard temperature and pressure, two atoms of the element bind to form dioxygen, a colorless and odorless diatomic gas with the formula . Diatomic oxygen gas currently constitutes 20.95% of the Earth's atmosphere, though this has changed considerably over long periods of time. Oxygen makes up almost half of the Earth's crust in the form of oxides.Atkins, P.; Jones, L.; Laverman, L. (2016).''Chemical Principles'', 7th edition. Freeman. Many major classes of organic molecules in living organisms contain oxygen atoms, such as proteins, nucleic acids, carbohydrates, and fats, as ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
Nitrogen
Nitrogen is the chemical element with the symbol N and atomic number 7. Nitrogen is a nonmetal and the lightest member of group 15 of the periodic table, often called the pnictogens. It is a common element in the universe, estimated at seventh in total abundance in the Milky Way and the Solar System. At standard temperature and pressure, two atoms of the element bond to form N2, a colorless and odorless diatomic gas. N2 forms about 78% of Earth's atmosphere, making it the most abundant uncombined element. Nitrogen occurs in all organisms, primarily in amino acids (and thus proteins), in the nucleic acids ( DNA and RNA) and in the energy transfer molecule adenosine triphosphate. The human body contains about 3% nitrogen by mass, the fourth most abundant element in the body after oxygen, carbon, and hydrogen. The nitrogen cycle describes the movement of the element from the air, into the biosphere and organic compounds, then back into the atmosphere. Many indus ... [...More Info...] [...Related Items...] OR: [Wikipedia] [Google] [Baidu] |
