1.
Myoglobin
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Myoglobin is an iron- and oxygen-binding protein found in the muscle tissue of vertebrates in general and in almost all mammals. It is related to hemoglobin, which is the iron- and oxygen-binding protein in blood, in humans, myoglobin is only found in the bloodstream after muscle injury. It is a finding, and can be diagnostically relevant when found in blood. Myoglobin is the primary oxygen-carrying pigment of muscle tissues, high concentrations of myoglobin in muscle cells allow organisms to hold their breath for a longer period of time. Diving mammals such as whales and seals have muscles with high abundance of myoglobin. Myoglobin is found in Type I muscle, Type II A and Type II B, myoglobin was the first protein to have its three-dimensional structure revealed by X-ray crystallography. This achievement was reported in 1958 by John Kendrew and associates, for this discovery, John Kendrew shared the 1962 Nobel Prize in chemistry with Max Perutz. They adapted to this deficiency through natural reactions to inadequate oxygen supply, in humans myoglobin is encoded by the MB gene. Hemoglobin can take the forms of oxyhemoglobin, carboxyhemoglobin, and methemoglobin, similarly, myoglobin can take the forms of oxymyoglobin, carboxymyoglobin, like hemoglobin, myoglobin is a cytoplasmic protein that binds oxygen on a heme group. It harbors only one group, whereas hemoglobin has four. Although its heme group is identical to those in Hb, Mb has an affinity for oxygen than does hemoglobin. This difference is related to its different role, whereas hemoglobin transports oxygen, myoglobin contains hemes, pigments responsible for the colour of red meat. The colour that meat takes is partly determined by the degree of oxidation of the myoglobin, in fresh meat the iron atom is the ferrous oxidation state bound to an oxygen molecule. Meat cooked well done is brown because the atom is now in the ferric oxidation state. If meat has been exposed to nitrites, it will remain pink because the atom is bound to NO. Grilled meats can also take on a smoke ring that comes from the iron binding to a molecule of carbon monoxide. Raw meat packed in a carbon monoxide atmosphere also shows this same pink smoke ring due to the same principles, notably, the surface of this raw meat also displays the pink color, which is usually associated in consumers minds with fresh meat. This artificially induced pink color can persist, reportedly up to one year, hormel and Cargill are both reported to use this meat-packing process, and meat treated this way has been in the consumer market since 2003
2.
Heme
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Not all porphyrins contain iron, but a substantial fraction of porphyrin-containing metalloproteins have heme as their prosthetic group, these are known as hemoproteins. Hemoproteins have diverse functions including the transportation of diatomic gases, chemical catalysis, diatomic gas detection. The heme iron serves as a source or sink of electrons during electron transfer or redox chemistry, in peroxidase reactions, the porphyrin molecule also serves as an electron source. In the transportation or detection of gases, the gas binds to the heme iron. During the detection of gases, the binding of the gas ligand to the heme iron induces conformational changes in the surrounding protein. Hemoproteins achieve their remarkable diversity by modifying the environment of the heme macrocycle within the protein matrix. For example, the ability of hemoglobin to effectively deliver oxygen to tissues is due to amino acid residues located near the heme molecule. Hemoglobin reversibly binds to oxygen in the lungs when the pH is high, when the situation is reversed, hemoglobin will release oxygen into the tissues. This phenomenon, which states that hemoglobins oxygen binding affinity is inversely proportional to both acidity and concentration of carbon dioxide, is known as the Bohr effect. There are several biologically important kinds of heme, The most common type is heme B, other important types include heme A, isolated hemes are commonly designated by capital letters while hemes bound to proteins are designated by lower case letters. Cytochrome a refers to the heme A in specific combination with membrane protein forming a portion of cytochrome c oxidase, the following carbon numbering system of porphyrins is an older numbering used by biochemists and not the 1–24 numbering system recommended by IUPAC which is shown in the table above. Heme l is the derivative of heme B which is attached to the protein of lactoperoxidase, eosinophil peroxidase. The addition of peroxide with the glutamyl-375 and aspartyl-225 of lactoperoxidase forms ester bonds between amino acid residues and the heme 1- and 5-methyl groups, respectively. Similar ester bonds with two methyl groups are thought to form in eosinophil and thyroid peroxidases. Heme l is one important characteristic of animal peroxidases, plant peroxidases incorporate heme B, lactoperoxidase and eosinophil peroxidase are protective enzymes responsible for the destruction of invading bacteria and virus. Thyroid peroxidase is the enzyme catalyzing the biosynthesis of the important thyroid hormones, because lactoperoxidase destroys invading organisms in the lungs and excrement, it is thought to be an important protective enzyme. Heme m is the derivative of heme B covalently bound at the site of myeloperoxidase. Heme m contains the two ester bonds at the heme 1- and 5-methyls as in heme l found in other mammalian peroxidases, myeloperoxidase is present in mammalian neutrophils and is responsible for the destruction of invading bacteria and viruse
3.
Oxygen
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Oxygen is a chemical element with symbol O and atomic number 8. It is a member of the group on the periodic table and is a highly reactive nonmetal. By mass, oxygen is the third-most abundant element in the universe, after hydrogen, at standard temperature and pressure, two atoms of the element bind to form dioxygen, a colorless and odorless diatomic gas with the formula O2. This is an important part of the atmosphere and diatomic oxygen gas constitutes 20. 8% of the Earths atmosphere, additionally, as oxides the element makes up almost half of the Earths crust. Most of the mass of living organisms is oxygen as a component of water, conversely, oxygen is continuously replenished by photosynthesis, which uses the energy of sunlight to produce oxygen from water and carbon dioxide. Oxygen is too reactive to remain a free element in air without being continuously replenished by the photosynthetic action of living organisms. Another form of oxygen, ozone, strongly absorbs ultraviolet UVB radiation, but ozone is a pollutant near the surface where it is a by-product of smog. At low earth orbit altitudes, sufficient atomic oxygen is present to cause corrosion of spacecraft, the name oxygen was coined in 1777 by Antoine Lavoisier, whose experiments with oxygen helped to discredit the then-popular phlogiston theory of combustion and corrosion. One of the first known experiments on the relationship between combustion and air was conducted by the 2nd century BCE Greek writer on mechanics, Philo of Byzantium. In his work Pneumatica, Philo observed that inverting a vessel over a burning candle, Philo incorrectly surmised that parts of the air in the vessel were converted into the classical element fire and thus were able to escape through pores in the glass. Many centuries later Leonardo da Vinci built on Philos work by observing that a portion of air is consumed during combustion and respiration, Oxygen was discovered by the Polish alchemist Sendivogius, who considered it the philosophers stone. In the late 17th century, Robert Boyle proved that air is necessary for combustion, English chemist John Mayow refined this work by showing that fire requires only a part of air that he called spiritus nitroaereus. From this he surmised that nitroaereus is consumed in both respiration and combustion, Mayow observed that antimony increased in weight when heated, and inferred that the nitroaereus must have combined with it. Accounts of these and other experiments and ideas were published in 1668 in his work Tractatus duo in the tract De respiratione. Robert Hooke, Ole Borch, Mikhail Lomonosov, and Pierre Bayen all produced oxygen in experiments in the 17th and the 18th century but none of them recognized it as a chemical element. This may have been in part due to the prevalence of the philosophy of combustion and corrosion called the phlogiston theory, which was then the favored explanation of those processes. Established in 1667 by the German alchemist J. J. Becher, one part, called phlogiston, was given off when the substance containing it was burned, while the dephlogisticated part was thought to be its true form, or calx. The fact that a substance like wood gains overall weight in burning was hidden by the buoyancy of the combustion products
4.
Protein Data Bank
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The Protein Data Bank is a crystallographic database for the three-dimensional structural data of large biological molecules, such as proteins and nucleic acids. The PDB is overseen by a called the Worldwide Protein Data Bank. The PDB is a key resource in areas of structural biology, 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. By 1971, one of Meyers programs, SEARCH, enabled researchers to access information from the database to study protein structures offline. SEARCH was instrumental in enabling networking, thus marking the beginning of the PDB. Upon Hamiltons death in 1973, Tom Koeztle took over direction of the PDB for the subsequent 20 years, in January 1994, Joel Sussman of Israels Weizmann Institute of Science was appointed head of the PDB. In October 1998, the PDB was transferred to the Research Collaboratory for Structural Bioinformatics, the new director was Helen M. Berman of Rutgers University. In 2003, with the formation of the wwPDB, the PDB became an international organization, the founding members are PDBe, RCSB, and PDBj. Each of the four members of wwPDB can act as deposition, data processing, the data processing refers to the fact that wwPDB staff review and annotate each submitted entry. The data are automatically checked for plausibility. The PDB database is updated weekly, likewise, the PDB holdings list is also updated weekly. As of 14 March 2017, the breakdown of current holdings is as follows,103,514 structures in the PDB have a structure factor file,9,057 structures have an NMR restraint file. 2,826 structures in the PDB have a chemical shifts file, therefore, the final conformation of the protein is obtained, in the latter case, by solving a distance geometry problem. A few proteins are determined by cryo-electron microscopy, the significance of the structure factor files, mentioned above, is that, for PDB structures determined by X-ray diffraction that have a structure file, the electron density map may be viewed. The data of such structures is stored on the electron density server, however, since 2007, the rate of accumulation of new protein structures appears to have plateaued. The file format used by the PDB was called the PDB file format. This original format was restricted by the width of computer punch cards to 80 characters per line, around 1996, the macromolecular Crystallographic Information file format, mmCIF, which is an extension of the CIF format started to be phased in
5.
Three-dimensional space
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Three-dimensional space is a geometric setting in which three values are required to determine the position of an element. This is the meaning of the term dimension. In physics and mathematics, a sequence of n numbers can be understood as a location in n-dimensional space, when n =3, the set of all such locations is called three-dimensional Euclidean space. It is commonly represented by the symbol ℝ3 and this serves as a three-parameter model of the physical universe in which all known matter exists. However, this space is one example of a large variety of spaces in three dimensions called 3-manifolds. Furthermore, in case, these three values can be labeled by any combination of three chosen from the terms width, height, depth, and breadth. In mathematics, analytic geometry describes every point in space by means of three coordinates. Three coordinate axes are given, each perpendicular to the two at the origin, the point at which they cross. They are usually labeled x, y, and z, below are images of the above-mentioned systems. Two distinct points determine a line. Three distinct points are either collinear or determine a unique plane, four distinct points can either be collinear, coplanar or determine the entire space. Two distinct lines can intersect, be parallel or be skew. Two parallel lines, or two intersecting lines, lie in a plane, so skew lines are lines that do not meet. Two distinct planes can either meet in a line or are parallel. Three distinct planes, no pair of which are parallel, can meet in a common line. In the last case, the three lines of intersection of each pair of planes are mutually parallel, a line can lie in a given plane, intersect that plane in a unique point or be parallel to the plane. In the last case, there will be lines in the plane that are parallel to the given line, a hyperplane is a subspace of one dimension less than the dimension of the full space. The hyperplanes of a space are the two-dimensional subspaces, that is
6.
Protein structure
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Protein structure is the three-dimensional arrangement of atoms in a protein molecule. Proteins are polymers — specifically polypeptides — formed from sequences of amino acids, 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, to understand the functions of proteins at a molecular level, it is often necessary to determine their three-dimensional structure. Protein structures range in size from tens to several amino acids. By physical size, proteins are classified as nanoparticles, between 1–100 nm, very large aggregates can be formed from protein subunits. For example, many thousands of actin molecules assemble into a microfilament, a protein may undergo reversible structural changes in performing its biological function. The alternative structures of the protein are referred to as different conformational isomers, or simply, conformations. There are four levels of protein structure. Each α-amino acid consists of a backbone that is present in all the amino acid types, an exception from this rule is proline. Because the carbon atom is bound to four different groups it is chiral, glycine however, is not chiral since its side chain is a hydrogen atom. A simple mnemonic for correct L-form is CORN, when the Cα atom is viewed with the H in front, the primary structure of a protein refers to the linear sequence of amino acids in the polypeptide chain. The primary structure is held together by covalent bonds such as peptide bonds, the two ends of the polypeptide chain are referred to as the carboxyl terminus and the amino terminus based on the nature of the free group on each extremity. Counting of residues always starts at the N-terminal end, which is the end where the group is not involved in a peptide bond. The primary structure of a protein is determined by the corresponding to the protein. A specific sequence of nucleotides in DNA is transcribed into mRNA, the sequence of amino acids in insulin was discovered by Frederick Sanger, establishing that proteins have defining amino acid sequences. The sequence of a protein is unique to that protein, and defines the structure, the sequence of a protein can be determined by methods such as Edman degradation or tandem mass spectrometry. Often, however, it is directly from the sequence of the gene using the genetic code
7.
Peptide
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Peptides are biologically occurring short chains of amino acid monomers linked by peptide bonds. The covalent chemical bonds are formed when the group of one amino acid reacts with the amine group of another. The shortest peptides are dipeptides, consisting of 2 amino acids joined by a peptide bond, followed by tripeptides, tetrapeptides. A polypeptide is a long, continuous, and unbranched peptide chain, hence, peptides fall under the broad chemical classes of biological oligomers and polymers, alongside nucleic acids, oligosaccharides and polysaccharides, etc. Peptides are distinguished from proteins on the basis of size, all peptides except cyclic peptides have an N-terminal and C-terminal residue at the end of the peptide. Ribosomal peptides Ribosomal peptides are synthesized by translation of mRNA and they are often subjected to proteolysis to generate the mature form. These function, typically in higher organisms, as hormones and signaling molecules, some organisms produce peptides as antibiotics, such as microcins. Since they are translated, the amino acid residues involved are restricted to those utilized by the ribosome, however, these peptides frequently have posttranslational modifications such as phosphorylation, hydroxylation, sulfonation, palmitoylation, glycosylation and disulfide formation. In general, they are linear, although lariat structures have been observed, more exotic manipulations do occur, such as racemization of L-amino acids to D-amino acids in platypus venom. Nonribosomal peptides Nonribosomal peptides are assembled by enzymes that are specific to each peptide, the most common non-ribosomal peptide is glutathione, which is a component of the antioxidant defenses of most aerobic organisms. Other nonribosomal peptides are most common in organisms, plants. These complexes are often out in a similar fashion. These peptides are often cyclic and can have highly complex cyclic structures, since the system is closely related to the machinery for building fatty acids and polyketides, hybrid compounds are often found. The presence of oxazoles or thiazoles often indicates that the compound was synthesized in this fashion, Peptones See also Tryptone Peptones are derived from animal milk or meat digested by proteolysis. In addition to containing small peptides, the material includes fats, metals, salts, vitamins. Peptones are used in nutrient media for growing bacteria and fungi, Peptide fragments Peptide fragments refer to fragments of proteins that are used to identify or quantify the source protein. Peptides received prominence in molecular biology for several reasons, the first is that peptides allow the creation of peptide antibodies in animals without the need of purifying the protein of interest. This involves synthesizing antigenic peptides of sections of the protein of interest and these will then be used to make antibodies in a rabbit or mouse against the protein
8.
Alpha helix
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This secondary structure is also sometimes called a classic Pauling–Corey–Branson α-helix. The name 3. 613-helix is also used for type of helix, denoting the average number of residues per helical turn. Among types of structure in proteins, the α-helix is the most regular. In the early 1930s, William Astbury showed that there were changes in the X-ray fiber diffraction of moist wool or hair fibers upon significant stretching. The data suggested that the unstretched fibers had a molecular structure with a characteristic repeat of ~5.1 ångströms. Astbury initially proposed a structure for the fibers. He later joined other researchers in proposing that, the protein molecules formed a helix the stretching caused the helix to uncoil. Hans Neurath was the first to show that Astburys models could not be correct in detail, neuraths paper and Astburys data inspired H. S. Taylor, Maurice Huggins and Bragg and collaborators to propose models of keratin that somewhat resemble the modern α-helix. The pivotal moment came in the spring of 1948, when Pauling caught a cold. Being bored, he drew a polypeptide chain of roughly correct dimensions on a strip of paper and folded it into a helix, after a few attempts, he produced a model with physically plausible hydrogen bonds. Pauling then worked with Corey and Branson to confirm his model before publication. The amino acids in an α-helix are arranged in a helical structure where each amino acid residue corresponds to a 100° turn in the helix. Dunitz describes how Paulings first article on the theme in fact shows a left-handed helix, short pieces of left-handed helix sometimes occur with a large content of achiral glycine amino acids, but are unfavorable for the other normal, biological L-amino acids. The pitch of the alpha-helix is 5.4 Å, which is the product of 1.5 and 3.6, the alpha-helices can be identified in protein structure using several computational methods, one of which being DSSP. Similar structures include the 310 helix and the π-helix, the subscripts refer to the number of atoms in the closed loop formed by the hydrogen bond. Residues in α-helices typically adopt backbone dihedral angles around, as shown in the image at right, in more general terms, they adopt dihedral angles such that the ψ dihedral angle of one residue and the φ dihedral angle of the next residue sum to roughly -105°. As a consequence, α-helical dihedral angles, in general, fall on a stripe on the Ramachandran diagram. For comparison, the sum of the angles for a 310 helix is roughly -75°
9.
Beta sheet
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The β-sheet is a common motif of regular secondary structure in proteins. Beta sheets consist of beta strands connected laterally by at least two or three 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 formation of the protein aggregates and fibrils observed in many human diseases, notably the amyloidoses such as Alzheimers disease. The first β-sheet structure was proposed by William Astbury in the 1930s and he proposed the idea of hydrogen bonding between the peptide bonds of parallel or antiparallel extended β-strands. However, Astbury did not have the data on the bond geometry of the amino acids in order to build accurate models. A refined version was proposed by Linus Pauling and Robert Corey in 1951 and their model incorporated the planarity of the peptide bond which they previously explained as resulting from keto-enol tautomerization. In the fully extended β-strand, successive side chains point straight up, then straight down, then straight up, adjacent β-strands in a β-sheet are aligned so that their Cα atoms are adjacent and their side chains point in the same direction. 5°. The pleating causes the distance between C α i and C i +2 α to be approximately 6 Å, rather than the 7.6 Å expected from two fully extended trans peptides, the sideways distance between adjacent Cα atoms in hydrogen-bonded β-strands is roughly 5 Å. However, β-strands are rarely extended, rather, they exhibit a twist due to the chirality of their component amino acids. The energetically preferred dihedral angles near = diverge significantly from the extended conformation =. The twist is often associated with alternating fluctuations in the angles to prevent the individual β-strands in a larger sheet from splaying apart. A good example of a strongly twisted β-hairpin can be seen in the protein BPTI, the side chains point outwards from the folds of the pleats, roughly perpendicularly to the plane of the sheet, successive residues point outwards on alternating faces of the sheet. Because peptide chains have a directionality conferred by their N-terminus and C-terminus and they are usually represented in protein topology diagrams by an arrow pointing toward the C-terminus. Adjacent β-strands can form hydrogen bonds in antiparallel, parallel, or mixed arrangements, in an antiparallel arrangement, the successive β-strands alternate directions so that the N-terminus of one strand is adjacent to the C-terminus of the next. The peptide backbone dihedral angles are about in antiparallel sheets, the dihedral angles are about in parallel sheets. For example, residue i may form bonds to residues j −1 and j +1. By contrast, residue j may hydrogen-bond to different residues altogether, finally, an individual strand may exhibit a mixed bonding pattern, with a parallel strand on one side and an antiparallel strand on the other. Also proteins are inherently constrained by folding kinetics as well as folding thermodynamics, the hydrogen bonding of β-strands need not be perfect, but can exhibit localized disruptions known as β-bulges
10.
Triosephosphate isomerase
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Triose-phosphate isomerase is an enzyme that catalyzes the reversible interconversion of the triose phosphate isomers dihydroxyacetone phosphate and D-glyceraldehyde 3-phosphate. Compound C00111 at KEGG Pathway Database. Enzyme 5.3.1.1 at KEGG Pathway Database. Compound C00118 at KEGG Pathway Database, TPI plays an important role in glycolysis and is essential for efficient energy production. TPI has been found in every organism searched for the enzyme, including animals such as mammals and insects as well as in fungi, plants. However, some bacteria that do not perform glycolysis, like ureaplasmas, in humans, deficiencies in TPI are associated with a progressive, severe neurological disorder called triose phosphate isomerase deficiency. Triose phosphate isomerase deficiency is characterized by hemolytic anemia. While there are mutations that cause this disease, most include the mutation of glutamic acid at position 104 to aspartic acid. Triose phosphate isomerase is an efficient enzyme, performing the reaction billions of times faster than it would occur naturally in solution. The reaction is so efficient that it is said to be perfect, It is limited only by the rate the substrate can diffuse into. The mechanism involves the formation of an enediol. The relative free energy of each state and transition state has been determined experimentally. The structure of TPI facilitates the conversion between dihydroxyacetone phosphate and glyceraldehyde 3-phosphate, the nucleophilic glutamate 165 residue of TPI deprotonates the substrate, and the electrophilic histidine 95 residue donates a proton to form the enediol intermediate. When deprotonated, the enediolate then collapses and, abstracting a proton from protonated glutamate 165, catalysis of the reverse reaction proceeds analogously, forming the same enediol but with enediolate collapse from the oxygen at C2. In terms of thermodynamics, DHAP formation is favored 20,1 over GAP production, however, in glycolysis, the use of GAP in the subsequent steps of metabolism drives the reaction toward its production. TPI is inhibited by sulfate, phosphate, and arsenate ions, other inhibitors include 2-phosphoglycolate, a transition state analog, and D-glycerol-1-phosphate, a substrate analog. Triose phosphate isomerase is a dimer of identical subunits, each of which is made up of about 250 amino acid residues, the three-dimensional structure of a subunit contains eight α-helices on the outside and eight parallel β-strands on the inside. In the illustration, the backbone of each subunit is colored in blue to red from N-terminus to C-terminus. This structural motif is called an αβ-barrel, or a TIM-barrel, the active site of this enzyme is in the center of the barrel. A glutamic acid residue and a histidine are involved in the catalytic mechanism, the sequence around the active site residues is conserved in all known triose phosphate isomerases
11.
Jane S. Richardson
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Jane Shelby Richardson is an American biophysicist who developed the Richardson diagram, or ribbon diagram, method of representing the 3D structure of proteins. She is a professor in biochemistry at Duke University, Richardson was born on January 25,1941 and grew up in Teaneck, New Jersey. Her father was an engineer and her mother was an English teacher. Her parents encouraged an interest in science and she was a member of local clubs as early as elementary school. She continued her education in science at Swarthmore College, enrolling with the intention of studying mathematics, astronomy, after finding herself unsuited to teaching high school, she joined her husband David C. Richardson, then completing his PhD work at MIT, in studying the 3-dimensional structure of the Staphylococcal nuclease protein by X-ray crystallography and it was one of the first dozen protein structures solved. She later began drawing her eponymous diagrams as a method of interpreting the structures of protein molecules and she has been promoted to many prestigious positions in academia. In July 1985 she was awarded a MacArthur Fellowship for her work in biochemistry and she was elected to the National Academy of Sciences and the American Academy of Arts and Sciences in 1991 and to the Institute of Medicine in 2006. She was elected president of the Biophysical Society for the 2012-2013 year, Richardson is currently a James B. Duke Professor of Biochemistry at Duke University, as part of her role in the National Academy of Sciences, Richardson serves on panels that advise the White House and Pentagon regarding nationally important scientific matters. The Richardsons jointly head a group at Duke University. Richardson is a contributor to Wikipedia, where she is a prominent member of WikiProject Biophysics, Richardsons first forays into science were in the field of astronomy. By observing the position of Sputnik – at the time, the only artificial satellite – on two nights, she managed to calculate its predicted orbit. She submitted her results to the Westinghouse Science Talent Search, winning third place in 1958, after earning her masters degree in philosophy, Richardson rejoined the scientific world in the mid 1960s, working as a technician in the same laboratory as her husband. Classes in botany and evolution that she had taken while pursuing her degree shaped her thinking about the work she was doing in the chemistry laboratory. During her crystallographic studies, Jane Richardson had come to realize that a classification scheme can be developed from the recurring structural motifs of the proteins. In 1977 she published her results in Nature, in a paper entitled β-sheet topology, in the meantime, Jane and David Richardson had moved to Duke University in 1970, where they solved the first crystal structure of superoxide dismutase. Richardson had developed the ribbon diagram over the course of her taxonomic research and her iconic images first appeared in the review journal Advances in Protein Chemistry in 1981, an early hallmark publication in structural bioinformatics
12.
Alpha and beta carbon
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The alpha carbon in organic molecules refers to the first carbon atom that attaches to a functional group, such as a carbonyl. The second carbon atom is called the beta carbon, and the system continues naming in alphabetical order with Greek letters, the nomenclature can also be applied to the hydrogen atoms attached to the carbon atoms. A hydrogen atom attached to a carbon atom is called an alpha-hydrogen atom, a hydrogen atom on the beta-carbon atom is a beta hydrogen atom. Organic molecules with more than one group can be a source of confusion. Generally the functional group responsible for the name or type of the molecule is the group for purposes of carbon-atom naming. For example, the molecules nitrostyrene and phenethylamine are very similar, alpha-carbon is also a term that applies to proteins and amino acids. It is the carbon before the carbonyl carbon. Therefore, reading along the backbone of a protein would give a sequence of –n– etc. The α-carbon is where the different substituents attach to different amino acid. That is, the groups hanging off the chain at the α-carbon are what give amino acids their diversity and these groups give the α-carbon its stereogenic properties for every amino acid except for glycine. Therefore, the α-carbon is a stereocenter for every amino acid except glycine, glycine also does not have a β-carbon, while every other amino acid does. The α-carbon of an acid is significant in protein folding. When describing a protein, which is a chain of amino acids, in general, α-carbons of adjacent amino acids in a protein are about 3.8 ångströms apart. The α-carbon is important for enol- and enolate-based carbonyl chemistry as well, an exception is in reaction with silyl- chlorides, -bromides, and -iodides, where the oxygen acts as the nucleophile to produce silyl enol ether. ^ Hackhs Chemical Dictionary,1969, page 30, ^ Hackhs Chemical Dictionary,1969, page 95
13.
Algorithm
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In mathematics and computer science, an algorithm is a self-contained sequence of actions to be performed. Algorithms can perform calculation, data processing and automated reasoning tasks, an algorithm is an effective method that can be expressed within a finite amount of space and time and in a well-defined formal language for calculating a function. The transition from one state to the next is not necessarily deterministic, some algorithms, known as randomized algorithms, giving a formal definition of algorithms, corresponding to the intuitive notion, remains a challenging problem. In English, it was first used in about 1230 and then by Chaucer in 1391, English adopted the French term, but it wasnt until the late 19th century that algorithm took on the meaning that it has in modern English. Another early use of the word is from 1240, in a manual titled Carmen de Algorismo composed by Alexandre de Villedieu and it begins thus, Haec algorismus ars praesens dicitur, in qua / Talibus Indorum fruimur bis quinque figuris. Which translates as, Algorism is the art by which at present we use those Indian figures, the poem is a few hundred lines long and summarizes the art of calculating with the new style of Indian dice, or Talibus Indorum, or Hindu numerals. An informal definition could be a set of rules that precisely defines a sequence of operations, which would include all computer programs, including programs that do not perform numeric calculations. Generally, a program is only an algorithm if it stops eventually, but humans can do something equally useful, in the case of certain enumerably infinite sets, They can give explicit instructions for determining the nth member of the set, for arbitrary finite n. An enumerably infinite set is one whose elements can be put into one-to-one correspondence with the integers, the concept of algorithm is also used to define the notion of decidability. That notion is central for explaining how formal systems come into being starting from a set of axioms. In logic, the time that an algorithm requires to complete cannot be measured, from such uncertainties, that characterize ongoing work, stems the unavailability of a definition of algorithm that suits both concrete and abstract usage of the term. Algorithms are essential to the way computers process data, thus, an algorithm can be considered to be any sequence of operations that can be simulated by a Turing-complete system. Although this may seem extreme, the arguments, in its favor are hard to refute. Gurevich. Turings informal argument in favor of his thesis justifies a stronger thesis, according to Savage, an algorithm is a computational process defined by a Turing machine. Typically, when an algorithm is associated with processing information, data can be read from a source, written to an output device. Stored data are regarded as part of the state of the entity performing the algorithm. In practice, the state is stored in one or more data structures, for some such computational process, the algorithm must be rigorously defined, specified in the way it applies in all possible circumstances that could arise. That is, any conditional steps must be dealt with, case-by-case
14.
Cubic function
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In algebra, a cubic function is a function of the form f = a x 3 + b x 2 + c x + d, where a is nonzero. Setting f =0 produces an equation of the form. The solutions of this equation are called roots of the polynomial f, If all of the coefficients a, b, c, and d of the cubic equation are real numbers then there will be at least one real root. All of the roots of the equation can be found algebraically. The roots can also be found trigonometrically, alternatively, numerical approximations of the roots can be found using root-finding algorithms like Newtons method. The coefficients do not need to be complex numbers, much of what is covered below is valid for coefficients of any field with characteristic 0 or greater than 3. The solutions of the cubic equation do not necessarily belong to the field as the coefficients. For example, some cubic equations with rational coefficients have roots that are complex numbers. Cubic equations were known to the ancient Babylonians, Greeks, Chinese, Indians, Babylonian cuneiform tablets have been found with tables for calculating cubes and cube roots. The Babylonians could have used the tables to solve cubic equations, the problem of doubling the cube involves the simplest and oldest studied cubic equation, and one for which the ancient Egyptians did not believe a solution existed. Methods for solving cubic equations appear in The Nine Chapters on the Mathematical Art, in the 3rd century, the Greek mathematician Diophantus found integer or rational solutions for some bivariate cubic equations. In the 11th century, the Persian poet-mathematician, Omar Khayyám, in an early paper, he discovered that a cubic equation can have more than one solution and stated that it cannot be solved using compass and straightedge constructions. He also found a geometric solution, in the 12th century, the Indian mathematician Bhaskara II attempted the solution of cubic equations without general success. However, he gave one example of an equation, x3 + 12x = 6x2 +35. He used what would later be known as the Ruffini-Horner method to approximate the root of a cubic equation. He also developed the concepts of a function and the maxima and minima of curves in order to solve cubic equations which may not have positive solutions. He understood the importance of the discriminant of the equation to find algebraic solutions to certain types of cubic equations. Leonardo de Pisa, also known as Fibonacci, was able to approximate the positive solution to the cubic equation x3 + 2x2 + 10x =20
15.
B-spline
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In the mathematical subfield of numerical analysis, a B-spline, or basis spline, is a spline function that has minimal support with respect to a given degree, smoothness, and domain partition. Any spline function of given degree can be expressed as a combination of B-splines of that degree. Cardinal B-splines have knots that are equidistant from each other, B-splines can be used for curve-fitting and numerical differentiation of experimental data. In the computer-aided design and computer graphics, spline functions are constructed as linear combinations of B-splines with a set of control points, the term B-spline was coined by Isaac Jacob Schoenberg and is short for basis spline. A spline function is a polynomial function of degree <k in a variable x. The places where the meet are known as knots. The number of internal knots must be equal to, or greater than k-1, thus the spline function has limited support. The key property of spline functions is that they are continuous at the knots, some derivatives of the spline function may also be continuous, depending on whether the knots are distinct or not. A B-spline of order n is a polynomial function of degree <n in a variable x. It is defined over a domain t 0 ≤ x ≤ tm, the points where x = tj are known as knots or break-points. The number of knots is equal to the degree of the polynomial if there are no knot multiplicities. The knots must be in ascending order, the number of knots is the minimum for the degree of the B-spline, which has a non-zero value only in the range between the first and last knot. Each piece of the function is a polynomial of degree <n between and including adjacent knots, a B-spline is a continuous function at the knots. When all internal knots are distinct, its derivatives are also continuous up to the derivative of degree n-1, if internal knots are coincident at a given value of x, the continuity of derivative order is reduced by 1 for each additional knot. For any given set of knots, the B-spline is unique, hence the name, B being short for Basis. The usefulness of B-splines lies in the fact that any function of order n on a given set of knots can be expressed as a linear combination of B-splines. This follows from the fact that all pieces have the same continuity properties, within their range of support. That is, B j,0 is piecewise constant one or zero indicating which knot span x is in, the corresponding Bs are zero outside those respective ranges
16.
Kinemage
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A kinemage is an interactive graphic scientific illustration. It often is used to visualize molecules, especially proteins although it can represent other types of 3-dimensional data. The kinemage system is designed to ease of use, interactive performance. The kinemage information is stored in a file, human- and machine-readable, that describes the hierarchy of display objects and their properties. The kinemage format is a defined chemical MIME type of chemical/x-kinemage with the file extension. kin, kinemages were first developed by David Richardson at Duke University School of Medicine, for the Protein Societys journal Protein Science that premiered in January 1992. Mage and RasMol were the first widely used macromolecular graphics programs to support interactive display on personal computers, kinemages are used for teaching, and for textbook supplements, individual exploration, and analysis of macromolecular structures. All-atom contact analysis adds and optimizes explicit hydrogen atoms, and then uses patches of dot surface to display the hydrogen bond, van der Waals, the interactive nature of kinemages is their primary purpose and attribute. To appreciate their nature, the demonstration KiNG in browser has two examples that can be moved around in 3D, plus instructions for how to embed a kinemage on a web page, the figure below shows KiNG being used to remodel a lysine sidechain in a high-resolution crystal structure. KiNG is one of the viewers provided on each page at the Protein Data Bank site. Kinemages can also be shown in immersive virtual reality systems, with the open-source KinImmerse software, all of the kinemage display and all-atom contact software is available free and open-source on the kinemage web site
17.
PyMOL
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PyMOL is computer software, a molecular visualization system created by Warren Lyford DeLano. It is user-sponsored, open-source software, released under the Python License and it is currently commercialized by Schrödinger, Inc. PyMOL can produce high-quality 3D images of small molecules and biological macromolecules, 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 is one of a few open-source model visualization tools available for use in structural biology, the Py part of the softwares name refers to that it extends, and is extensible by, the programming language Python. PyMOL uses OpenGL Extension Wrangler Library and Freeglut, and can solve Poisson–Boltzmann equations using the Adaptive Poisson Boltzmann Solver, PyMOL uses Tk for the GUI widgets, Native Aqua binaries are available for macOS through Schrödinger. On 1 August 2006, DeLano Scientific adopted a controlled-access download system for precompiled PyMOL builds distributed by the company, access to these executables is now limited to registered users who are paying customers, educational builds are available free to students and teachers. However, most of the current source code continues to be available for free, while the build systems for other platforms are open, the Windows API build system is not, although unofficial Windows binaries are available online. Anyone can either compile an executable from the code or pay for a subscription to support services to obtain access to precompiled executables. On 8 January 2010, Schrödinger, Inc. reached an agreement to acquire PyMOL, the firm assumed development, maintenance, support, and sales of PyMOL, including all then-valid subscriptions. They also continue to support the PyMOL open-source community
18.
Tubby protein
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The tubby protein is encoded by the TUB gene. It is a cell signaling protein common to multicellular eukaryotes. The first tubby gene was identified in mice, and proteins that are homologous to tubby are known as tubby-like proteins and they share a common and characteristic tertiary structure that consists of a beta barrel packed around an alpha helix in the central pore. The gene derives its name from its role in metabolism, mice with a mutated tubby gene develop delayed-onset obesity, sensorineural hearing loss, Tubby proteins are classified as α+β proteins and have a 12-beta stranded barrel surrounding a central alpha helix. Tubby proteins can bind the cell signaling molecule phosphatidylinositol, which is typically localized to the cell membrane. A similar structural fold to the Tubby like proteins has been identified in the Scramblase family of proteins, Tubby proteins have been implicated as transcription factors and as potential signaling factors coupled to G-protein activity. They are associated with neuronal differentiation and development, and in mammals are implicated in three disease processes when mutated, obesity, retinal degeneration, and hearing loss, in mice, mutations in tubby proteins are known to affect life span and fat storage as well as carbohydrate metabolism. Tubby domains associate with cytoplasmic side of cell membranes through binding of different phosphoinositides TUB, TULP1, TULP2, TULP3, TULP4, SCOP tubby fold
19.
Jmol
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Jmol is computer software for molecular modelling chemical structures in 3-dimensions. Jmol returns a 3D representation of a molecule that may be used as a teaching tool and it is written in the programming language Java, so it can run on the operating systems Windows, macOS, Linux, and Unix, if Java is installed. It is free and open-source software released under a GNU Lesser General Public License version 2.0, a standalone application and a software development kit exist that can be integrated into other Java applications, such as Bioclipse and Taverna. A popular feature is an applet that can be integrated into web pages to display molecules in a variety of ways, for example, molecules can be displayed as ball-and-stick models, space-filling models, ribbon diagrams, etc. Jmol supports a range of chemical file formats, including Protein Data Bank, Crystallographic Information File, MDL Molfile. There is also a JavaScript-only version, JSmol, that can be used on computers with no Java, the Jmol applet, among other abilities, offers an alternative to the Chime plug-in, which is no longer under active development. While Jmol has many features that Chime lacks, it does not claim to reproduce all Chime functions, most notably, Chime requires plug-in installation and Internet Explorer 6.0 or Firefox 2.0 on Microsoft Windows, or Netscape Communicator 4.8 on Mac OS9. Jmol requires Java installation and operates on a variety of platforms. For example, Jmol is fully functional in Mozilla Firefox, Internet Explorer, Opera, Google Chrome, fast and Scriptable Molecular Graphics in Web Browsers without Java3D
20.
UCSF Chimera
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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 at the University of California, San Francisco. Development is funded by the National Institutes of Health, the next-generation program UCSF ChimeraX is under development. Prerelease daily builds with current capabilities are available for Mac, Linux, development is funded by the National Institutes of Health
21.
Scientific visualization
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Scientific visualization is an interdisciplinary branch of science. It is also considered a subset of computer graphics, a branch of computer science, the purpose of scientific visualization is to graphically illustrate scientific data to enable scientists to understand, illustrate, and glean insight from their data. One of the earliest examples of scientific visualisation was Maxwells thermodynamic surface. This prefigured modern scientific techniques that use computer graphics. Scientific visualization using computer graphics gained in popularity as graphics matured, primary applications were scalar fields and vector fields from computer simulations and also measured data. The primary methods for visualizing two-dimensional scalar fields are color mapping and drawing contour lines, 2D vector fields are visualized using glyphs and streamlines or line integral convolution methods. For 3D scalar fields the primary methods are volume rendering and isosurfaces, methods for visualizing vector fields include glyphs such as arrows, streamlines and streaklines, particle tracing, line integral convolution and topological methods. Later, visualization techniques such as hyperstreamlines were developed to visualize 2D, computer animation is the art, technique, and science of creating moving images via the use of computers. It is becoming common to be created by means of 3D computer graphics, though 2D computer graphics are still widely used for stylistic, low bandwidth. Sometimes the target of the animation is the computer itself, but sometimes the target is another medium and it is also referred to as CGI, especially when used in films. Computer simulation is a program, or network of computers. The simultaneous visualization and simulation of a system is called visulation, computer simulations vary from computer programs that run a few minutes, to network-based groups of computers running for hours, to ongoing simulations that run for months. Information visualization focused on the creation of approaches for conveying information in intuitive ways. The key difference between scientific visualization and information visualization is that information visualization is often applied to data that is not generated by scientific inquiry, some examples are graphical representations of data for business, government, news and social media. Interface technology and perception shows how new interfaces and an understanding of underlying perceptual issues create new opportunities for the scientific visualization community. Rendering is the process of generating an image from a model, the model is a description of three-dimensional objects in a strictly defined language or data structure. It would contain geometry, viewpoint, texture, lighting, the image is a digital image or raster graphics image. The term may be by analogy with a rendering of a scene
22.
Electron microscope
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An electron microscope is a microscope that uses a beam of accelerated electrons as a source of illumination. Transmission electron microscopes use electrostatic and electromagnetic lenses to control the electron beam and these electron optical lenses are analogous to the glass lenses of an optical light microscope. Industrially, electron microscopes are used for quality control and failure analysis. Modern electron microscopes produce electron micrographs using specialized digital cameras and frame grabbers to capture the image, the first electromagnetic lens was developed in 1926 by Hans Busch. According to Dennis Gabor, the physicist Leó Szilárd tried in 1928 to convince Busch to build an electron microscope, two years later, in 1933, Ruska built an electron microscope that exceeded the resolution attainable with an optical microscope. Moreover, Reinhold Rudenberg, the director of Siemens-Schuckertwerke, obtained the patent for the electron microscope in May 1931. In 1932, Ernst Lubcke of Siemens & Halske built and obtained images from an electron microscope. Five years later, the firm financed the work of Ernst Ruska and Bodo von Borries, also in 1937, Manfred von Ardenne pioneered the scanning electron microscope. The first commercial electron microscope was produced in 1938 by Siemens, although contemporary transmission electron microscopes are capable of two million-power magnification, as scientific instruments, they remain based upon Ruska’s prototype. The original form of electron microscope, the electron microscope uses a high voltage electron beam to illuminate the specimen. The electron beam is produced by a gun, commonly fitted with a tungsten filament cathode as the electron source. When it emerges from the specimen, the electron beam carries information about the structure of the specimen that is magnified by the lens system of the microscope. The image detected by the camera may be displayed on a monitor or computer. The resolution of TEMs is limited primarily by spherical aberration, but a new generation of aberration correctors have been able to partially overcome spherical aberration to increase resolution. The ability to determine the positions of atoms within materials has made the HRTEM an important tool for nano-technologies research, transmission electron microscopes are often used in electron diffraction mode. The major disadvantage of the electron microscope is the need for extremely thin sections of the specimens. Biological specimens are required to be chemically fixed, dehydrated and embedded in a polymer resin to stabilize them sufficiently to allow ultrathin sectioning. Sections of biological specimens, organic polymers and similar materials may require treatment with heavy atom labels in order to achieve the required image contrast
23.
Python (programming language)
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Python is a widely used high-level programming language for general-purpose programming, created by Guido van Rossum and first released in 1991. The language provides constructs intended to enable writing clear programs on both a small and large scale and it has a large and comprehensive standard library. Python interpreters are available for operating systems, allowing Python code to run on a wide variety of systems. CPython, the implementation of Python, is open source software and has a community-based development model. CPython is managed by the non-profit Python Software Foundation, about the origin of Python, Van Rossum wrote in 1996, Over six years ago, in December 1989, I was looking for a hobby programming project that would keep me occupied during the week around Christmas. Would be closed, but I had a computer. I decided to write an interpreter for the new scripting language I had been thinking about lately, I chose Python as a working title for the project, being in a slightly irreverent mood. Python 2.0 was released on 16 October 2000 and had major new features, including a cycle-detecting garbage collector. With this release the development process was changed and became more transparent, Python 3.0, a major, backwards-incompatible release, was released on 3 December 2008 after a long period of testing. Many of its features have been backported to the backwards-compatible Python 2.6. x and 2.7. x version series. The End Of Life date for Python 2.7 was initially set at 2015, many other paradigms are supported via extensions, including design by contract and logic programming. Python uses dynamic typing and a mix of reference counting and a garbage collector for memory management. An important feature of Python is dynamic name resolution, which binds method, the design of Python offers some support for functional programming in the Lisp tradition. The language has map, reduce and filter functions, list comprehensions, dictionaries, and sets, the standard library has two modules that implement functional tools borrowed from Haskell and Standard ML. Python can also be embedded in existing applications that need a programmable interface, while offering choice in coding methodology, the Python philosophy rejects exuberant syntax, such as in Perl, in favor of a sparser, less-cluttered grammar. As Alex Martelli put it, To describe something as clever is not considered a compliment in the Python culture. Pythons philosophy rejects the Perl there is more one way to do it approach to language design in favor of there should be one—and preferably only one—obvious way to do it. Pythons developers strive to avoid premature optimization, and moreover, reject patches to non-critical parts of CPython that would offer an increase in speed at the cost of clarity
24.
PubMed Identifier
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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 at the National Institutes of Health maintains the database as part of the Entrez system of information retrieval, from 1971 to 1997, MEDLINE online access to the MEDLARS Online computerized database primarily had been through institutional facilities, such as university libraries. PubMed, first released in January 1996, ushered in the era of private, free, home-, the PubMed system was offered free to the public in June 1997, when MEDLINE searches via the Web were demonstrated, in a ceremony, by Vice President Al Gore. Information about the journals indexed in MEDLINE, and available through PubMed, is found in the NLM Catalog. As of 5 January 2017, PubMed has more than 26.8 million records going back to 1966, selectively to the year 1865, and very selectively to 1809, about 500,000 new records are added each year. As of the date,13.1 million of PubMeds records are listed with their abstracts. In 2016, NLM changed the system so that publishers will be able to directly correct typos. Simple searches on PubMed can be carried out by entering key aspects of a subject into PubMeds search window, when a journal article is indexed, numerous article parameters are extracted and stored as structured information. Such parameters are, Article Type, Secondary identifiers, Language, publication type parameter enables many special features. As these clinical girish can generate small sets of robust studies with considerable precision, since July 2005, the MEDLINE article indexing process extracts important identifiers from the article abstract and puts those in a field called Secondary Identifier. The secondary identifier field is to store numbers to various databases of molecular sequence data, gene expression or chemical compounds. For clinical trials, PubMed extracts trial IDs for the two largest trial registries, ClinicalTrials. gov and the International Standard Randomized Controlled Trial Number Register, a reference which is judged particularly relevant can be marked and related articles can be identified. If relevant, several studies can be selected and related articles to all of them can be generated using the Find related data option, the related articles are then listed in order of relatedness. To create these lists of related articles, PubMed compares words from the title and abstract of each citation, as well as the MeSH headings assigned, using a powerful word-weighted algorithm. The related articles function has been judged to be so precise that some researchers suggest it can be used instead of a full search, a strong feature of PubMed is its ability to automatically link to MeSH terms and subheadings. Examples would be, bad breath links to halitosis, heart attack to myocardial infarction, where appropriate, these MeSH terms are automatically expanded, that is, include more specific terms. Terms like nursing are automatically linked to Nursing or Nursing and this important feature makes PubMed searches automatically more sensitive and avoids false-negative hits by compensating for the diversity of medical terminology. The My NCBI area can be accessed from any computer with web-access, an earlier version of My NCBI was called PubMed Cubby
25.
International Standard Book Number
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The International Standard Book Number is a unique numeric commercial book identifier. An ISBN is assigned to each edition and variation of a book, for example, an e-book, a paperback and a hardcover edition of the same book would each have a different ISBN. The ISBN is 13 digits long if assigned on or after 1 January 2007, the method of assigning an ISBN is nation-based and varies from country to country, often depending on how large the publishing industry is within a country. The initial ISBN configuration of recognition was generated in 1967 based upon the 9-digit Standard Book Numbering created in 1966, the 10-digit ISBN format was developed by the International Organization for Standardization and was published in 1970 as international standard ISO2108. Occasionally, a book may appear without a printed ISBN if it is printed privately or the author does not follow the usual ISBN procedure, however, this can be rectified later. Another identifier, the International Standard Serial Number, identifies periodical publications such as magazines, the ISBN configuration of recognition was generated in 1967 in the United Kingdom by David Whitaker and in 1968 in the US by Emery Koltay. The 10-digit ISBN format was developed by the International Organization for Standardization and was published in 1970 as international standard ISO2108, the United Kingdom continued to use the 9-digit SBN code until 1974. The ISO on-line facility only refers back to 1978, an SBN may be converted to an ISBN by prefixing the digit 0. For example, the edition of Mr. J. G. Reeder Returns, published by Hodder in 1965, has SBN340013818 -340 indicating the publisher,01381 their serial number. This can be converted to ISBN 0-340-01381-8, the check digit does not need to be re-calculated, since 1 January 2007, ISBNs have contained 13 digits, a format that is compatible with Bookland European Article Number EAN-13s. An ISBN is assigned to each edition and variation of a book, for example, an ebook, a paperback, and a hardcover edition of the same book would each have a different ISBN. The ISBN is 13 digits long if assigned on or after 1 January 2007, a 13-digit ISBN can be separated into its parts, and when this is done it is customary to separate the parts with hyphens or spaces. Separating the parts of a 10-digit ISBN is also done with either hyphens or spaces, figuring out how to correctly separate a given ISBN number is complicated, because most of the parts do not use a fixed number of digits. ISBN issuance is country-specific, in that ISBNs are issued by the ISBN registration agency that is responsible for country or territory regardless of the publication language. Some ISBN registration agencies are based in national libraries or within ministries of culture, in other cases, the ISBN registration service is provided by organisations such as bibliographic data providers that are not government funded. In Canada, ISBNs are issued at no cost with the purpose of encouraging Canadian culture. In the United Kingdom, United States, and some countries, where the service is provided by non-government-funded organisations. Australia, ISBNs are issued by the library services agency Thorpe-Bowker
26.
Science (journal)
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Science, also widely referred to as Science Magazine, is the peer-reviewed academic journal of the American Association for the Advancement of Science and one of the worlds top academic journals. It was first published in 1880, is circulated weekly and has a print subscriber base of around 130,000. Because institutional subscriptions and online access serve an audience, its estimated readership is 570,400 people. Unlike most scientific journals, which focus on a field, Science. According to the Journal Citation Reports, Sciences 2015 impact factor was 34.661, although it is the journal of the AAAS, membership in the AAAS is not required to publish in Science. Papers are accepted from authors around the world, competition to publish in Science is very intense, as an article published in such a highly cited journal can lead to attention and career advancement for the authors. Fewer than 7% of articles submitted are accepted for publication, Science is based in Washington, D. C. United States, with an office in Cambridge, England. Science was founded by New York journalist John Michels in 1880 with financial support from Thomas Edison, however, the journal never gained enough subscribers to succeed and ended publication in March 1882. Entomologist Samuel H. Scudder resurrected the journal one year later and had some success while covering the meetings of prominent American scientific societies, however, by 1894, Science was again in financial difficulty and was sold to psychologist James McKeen Cattell for $500. In an agreement worked out by Cattell and AAAS secretary Leland O. Howard, after Cattell died in 1944, the ownership of the journal was transferred to the AAAS. After Cattells death in 1944, the journal lacked a consistent editorial presence until Graham DuShane became editor in 1956. In 1958, under DuShanes leadership, Science absorbed The Scientific Monthly, physicist Philip Abelson, a co-discoverer of neptunium, served as editor from 1962 to 1984. Under Abelson the efficiency of the process was improved and the publication practices were brought up to date. During this time, papers on the Apollo program missions and some of the earliest reports on AIDS were published, biochemist Daniel E. Koshland, Jr. served as editor from 1985 until 1995. From 1995 until 2000, neuroscientist Floyd E. Bloom held that position, biologist Donald Kennedy became the editor of Science in 2000. Biochemist Bruce Alberts took his place in March 2008, geophysicist Marcia McNutt became editor-in-chief in June 2013. During her tenure the family of journals expanded to include Science Robotics and Science Immunology, jeremy M. Berg became editor-in-chief on July 1,2016
, PMID 1304880
