Secondarystructure prediction is a set of techniques in bioinformatics that aim to predict the secondarystructure s of protein s and nucleic acid sequences based only on knowledge of their primary structure . For proteins, this means predicting the formation of protein structure s such as alpha helix alpha helices and beta sheet beta strand s, while for nucleic acids it means predicting the formation of nucleic acid structure s like helixes and stem loop structures through base pair ing and base stacking interactions. Secondarystructure prediction can refer to Protein structure prediction Secondarystructure Protein structure prediction Secondarystructure Nucleic acid structure prediction disambig ... more details
in 1962. In biochemistry and structural biology , secondarystructure is the general three dimensional ... structure . Secondarystructure can be formally defined by the hydrogen bond s of the biopolymer, as observed in an atomic resolution structure. In proteins, the secondarystructure is defined ..., the secondarystructure is defined by the hydrogen bonding between the nitrogenous bases. The hydrogen ... of secondarystructure difficult. The secondarystructure may be also defined based on the regular ... hydrogen bonds. The secondarystructure may be also provided by crystallographers in the corresponding Protein Data Bank file format PDB file. The rough secondarystructure content of a biopolymer ... oscillations of amide groups due to hydrogen bonding. Finally, secondarystructure contents may ... spectrum. Secondarystructure was introduced by Kaj Ulrik Linderstr m Lang at Stanford in 1952. Protein ... and loose, flexible loops link the more regular secondarystructure elements. The random coil is not a true secondarystructure, but is the class of conformations that indicate an absence of regular secondarystructure. Amino acid s vary in their ability to form the various secondarystructure elements ... a reliable method of predicting secondarystructure from sequence alone. There are several methods for defining protein secondarystructure e.g. DEFINE, ref cite journal title Identification of structural motifs from protein coordinate data secondarystructure and first level supersecondary ... secondarystructure pattern recognition of hydrogen bonded and geometrical features journal Biopolymers ... based protein secondarystructure assignment journal Proteins year 1995 volume 23 number 4 pages ... March 2006 Secondarystructure assigned by DSSP 8 conformational states reduced to 3 states H HGI, E ... states The Dictionary of Protein SecondaryStructure, in short DSSP, is commonly used to describe the protein secondarystructure with single letter codes. The secondarystructure is assigned based ... more details
The secondarystructure of a nucleic acid molecule refers to the basepair ing interactions within a single ... context, secondarystructure is a vital consideration in the Nucleic acid design rational design of nucleic ... of sequence reading enzymes such as DNA polymerase . Secondarystructure motifs Nucleic acid secondary ... in nuleic acid molecules which is intimately connected with the molecule s secondarystructure ... An example of an RNA stem loop secondarystructure Main Stem loop The secondarystructure of nucleic ... in the opposite strand are also frequent. There are many secondarystructure elements of functional ... attempting to determine the secondarystructure of RNA molecules. Approaches include both Nucleic acid ... secondarystructure containing at least two stem loop structures in which half of one stem is intercalated ... the presence of general pseudoknots in RNA sequences impossible to secondarystructure prediction ..., they are generally not present in biological DNA. Secondarystructure prediction Main Nucleic acid structure prediction One application of bioinformatics uses predicted RNA secondary structures in searching ... probable RNA secondarystructure is dynamic programming , although this has the disadvantage that it cannot ..., the secondarystructure is highly important to the correct function of the RNA &mdash often ... RNA genes . RNA secondarystructure can be predicted with some accuracy by computer and many bioinformatics applications use some notion of secondarystructure in analysis of RNA. See also DNA nanotechnology ... DEFAULTSORT Nucleic Acid SecondaryStructure Category DNA Category Biophysics Category Molecular ... pmid 14990744 pmc 390280 ref The secondary structures of biological DNA s and RNA s tend to be different ... ultimately determines the overall structure of the molecules. Fundamental concepts Base pairing multiple ... and functional nucleic acid tertiary structure tertiary structures . Importantly, pairing is the mechanism ... helix double helical structure held together by base pair s. align right class wikitable Melting ... more details
In mathematics , particularly differential topology , the secondary vector bundle structure refers to the natural vector bundle structure TE , p sub sub , TM on the total space TE of the tangent bundle of a smooth vector bundle E , p , M , induced by the push forward p sub sub TE &rarr TM of the original projection map p E &rarr M . In the special case E , p , M TM ,&pi sub TM sub , M , where TE TTM is the double tangent bundle , the secondary vector bundle TTM , &pi sub TM sub sub sub , TM is isomorphic to the tangent bundle TTM ,&pi sub TTM sub , TM of TM through the double tangent bundle canonical flip . Construction of the secondary vector bundle structure Let E , p , M be a smooth vector bundle of rank N . Then the preimage p sub sub sup 1 sup X TE of any tangent vector X &isin TM in the push forward p sub sub TE &rarr TM of the canonical projection p E &rarr M is a smooth submanifold of dimension 2 N , and it becomes a vector space with the push forwards math T E times E to TE quad , quad lambda TE to TE math of the original addition and scalar multiplication math E times E to E qquad , qquad lambda E to E math as its vector space operations. The triple TE , p sub sub , TM becomes a smooth vector bundle with these vector space operations on its fibres. Proof Let U ,&phi be a local coordinate system on the base manifold M with &phi x x sup 1 sup ,..., x sup n sup and let math psi W to varphi U times mathbb R N quad quad psi v k e k x x 1, ldots,x n,v 1, ldots,v N math be a coordinate system on E adapted to it. Then math p Big X k frac partial partial x k Big v Y ell frac partial partial v ell Big v Big X k frac partial partial x k Big p v , math so the fiber of the secondary vector bundle structure at X &isin T sub x sub M is of the form math p 1 X Big X k frac partial ... if the connector map is linear with respect to the secondary vector bundle structure TE , p ... linear with respect to the tangent bundle structure TE ,&pi sub TE sub , E . See also Connection ... more details
Summary Information Description ENOD40 RNA secondarystructure and sequence conservation Source I User Ppgardne Paul User talk Ppgardne talk created this work entirely by myself. Date 08 58, 24 October 2010 UTC Author User Ppgardne Paul User talk Ppgardne talk other versions Licensing self cc by sa 3.0 GFDL migration redundant Copy to Wikimedia Commons bot Fbot priority true ... more details
Summary Information Description RNA secondarystructure and sequence conservation for miR 96 Source I created this work entirely by myself. Date 02 May 2009 Author User Ppgardne Paul User talk Ppgardne talk Licensing PD self date May 2009 Orphan image Copy to Wikimedia Commons bot Fbot ... more details
Summary Information Description RNA secondarystructure and sequence conservation for miR 96 Source I created this work entirely by myself. Date 02 May 2009 Author User Ppgardne Paul User talk Ppgardne talk Licensing PD self date May 2009 Copy to Wikimedia Commons bot Fbot priority true ... more details
Summary Information Description Rho independent terminator sequence and secondarystructure conservation Source I created this work entirely by myself. Date 2009 05 07 Author User Ppgardne Paul User talk Ppgardne talk other versions Licensing self cc by sa 3.0 GFDL Copy to Wikimedia Commons bot Fbot priority true ... more details
Information Description Secondarystructure and sequence conservation for 6C RNA Source I created this work entirely by myself. Date 16 06 09 Author User Ppgardne Paul User talk Ppgardne talk 21 04, 16 May 2009 UTC GFDL migration relicense ... more details
Author TANGDJ. Multiple alignment was done by using ClustalW program and the consensus secondarystructure was predicted based on the multiple alignment using RNAalifold program. Licensing self cc by sa 3.0 GFDL migration redundant Copy to Wikimedia Commons bot Fbot ... more details
Wiktionarypar secondarySecondary is an adjective meaning second or second hand . It may refer to The group of usually at least four defensive back s in American football and Canadian football An obsolete name for the Mesozoic in geosciences The secondary winding, or the electrical or electronic circuit connected to the secondary winding in a transformer Secondary color Secondary consumers in ecology Trophic dynamics Secondary dominant in music Secondary education Secondary school The type of school at the secondary level of education Secondary market , an aftermarket where financial assets are traded Secondary market offering Secondary mirror , second mirror element focusing surface in a reflecting telescope Secondary neoplasm Secondaries, the second largest group of remiges wing feathers , which attach to the inner lower arm Private equity secondary , investment in an existing private equity fund or other alternative asset disambig es Secundario fr Secondaire ... more details
and RNA . The structure of these molecules is frequently decomposed into primary structure, secondary ... recognizable domains of protein structure and nucleic acid structure , including secondarystructure ... and beta sheet s for proteins. The terms primary, secondary, tertiary, and quaternary structure were ... The family of box ACA small nucleolar RNAs is defined by an evolutionarily conserved secondarystructure ... doi 10.1016 0092 8674 81 90522 5 ref Secondarystructure Main Protein secondarystructure Nucleic acid secondarystructure image TRNA all2.png 250px thumb right alt Colored dice with checkered background Secondary inset and tertiary structure of tRNA demonstrating coaxial stacking. PDB http www.ncbi.nlm.nih.gov ... and structural biology , secondarystructure is the general three dimensional form of local ... tertiary structure . Secondarystructure is formally defined by the hydrogen bond s of the biopolymer, as observed in an atomic resolution structure. In proteins, the secondarystructure is defined ... bond is used. In nucleic acids, the secondarystructure is defined by the hydrogen bonding between ... features, which has given rise to less formal definitions of secondarystructure. For example ... assign its secondarystructure by eye and record their assignments in the corresponding Protein Data Bank file format PDB file. The secondarystructure of a nucleic acid molecule refers to the basepair ing interactions within a single molecule or set of interacting molecules. The secondarystructure ... loop s. There are many secondarystructure elements of functional importance to biological ... the secondarystructure of RNA molecules. Approaches include both Nucleic acid structure determination ... base sequence. In other words, it is the prediction of secondary and tertiary structure from its primary .... However, in the case of RNA much of the final structure is determined by the secondarystructure ... of Base pair base pairings across diverse species. Secondarystructure of small nucleic acid ... more details
A supersecondary structure is a compact three dimensional protein structure of several adjacent elements of secondarystructure that is smaller than a protein domain or a protein subunit subunit . Supersecondary structures can act as nucleation s in the process of protein folding . Examples include Beta hairpin hairpins , helix hairpins, and motifs. See also Structural motif Further reading cite journal author Chiang YS, Gelfand TI, Kister AE, Gelfand IM title New classification of supersecondary structures of sandwich like proteins uncovers strict patterns of strand assemblage. journal Proteins. volume 68 issue 4 pages 915 921 year 2007 pmid 17557333 doi 10.1002 prot.21473 DEFAULTSORT Supersecondary Structure Category Protein structural motifs ... more details
, the residues read CO R N in a clockwise direction. Secondarystructure File Alpha helix.png thumb right 100px An alpha helix with hydrogen bonds yellow dots Main Protein secondarystructureSecondarystructure refers to highly regular local sub structures. Two main types of secondarystructure ... polypeptide chain lacking any fixed three dimensional structure. Several sequential secondary ... refers to a specific combination of secondarystructure elements, such as beta alpha beta units ... super secondarystructure protein database http bioinformatics.eas.asu.edu springs Sprouts projectsSprouts.html ... necessary to determine their three dimensional structure. This is the topic of the scientific field ... , and dual polarisation interferometry to determine the structure of proteins. Protein structures ... conformational change s. Protein covalent structure and stereochemistry Image a amino acid.png .... These properties play a major role in molding protein structure. The peptide bond Image 2 amino ... s conformation. They are restrained by geometry to allowed ranges typical for particular secondarystructure elements, and represented in a Ramachandran plot . A few important bond length s are given ... Libraries ref Levels of protein structure File Main protein structure levels en.svg thumb left 250px Protein structure , from primary to quaternary structure. There are four distinct levels of protein structure. Primary structure Main Protein primary structure The primary structure refers to amino acid sequence of the polypeptide chain. The primary structure is held together by Covalent bond covalent ... in a peptide bond. The primary structure of a protein is determined by the gene corresponding ... is unique to that protein, and defines the structure and function of the protein. The sequence ... and glycosylations are usually also considered a part of the primary structure, and cannot ... year 1951 volume 37 issue 4 pages 205 211 title The structure of proteins two hydrogen bonded helical ... more details
orphan date September 2010 A dish structure is a secondary sedimentary structure caused by liquefaction and fluidization of the soft sediment deposition soft sediment . The structure occurs mainly in clastic ..., the structure is recognized as penecontemporaneous or secondary , formed during the dewatering of rapidly ... 300px Dish structure from Northern California Due to the similarity in its shape to a Plate dishware dish , the structure, sometimes also referred to as dish and pillar or dish and pipe , was named after the common kitchen item. History Dish structure was described scientifically for the first time ... C. M. Wentworth 1967 . Dish structure, a primary sedimentary structure and coarse turbidites. Am. Assoc ..., 22 , p. 157 204 ref . Description Image Dish structure.jpg thumb 200px Sketched dish structure .... Upturned edge of a dish in blue. The subhorizontal dish structure consists of two parts, the dish ... Image DishStructureTalara.jpg thumb 300px left Giant dish structure near Talara, Peru Dish structure occurs in laterally extensive sheets. The medium in which the structure forms is usually coarse ... beds are normally graded. The depositional environment of the structure is mainly deep ... concentration flows grain flows, fluidized flows, liquefied flows . But dish structure can also be encountered ... ref T. H. Nilsen et al. 1977 . New occurrence of dish structure in the stratigraphic record ... ash layers within marine sediments. In turbidites dish structure usually forms within Bouma sequence Bouma C , occasionally also within Bouma B. Good examples of dish structure can be seen for instance ... Chile . Some of the largest dish structure is found near Talara in northern Peru . Formation Up to 1974 dish structure was still regarded as a primary sedimentary structure . The formation of the structure ... ref . The postdepositional character of dish structure can sometimes clearly be seen in cut or displaced ... forceful upward flow creates pillars which are essentially dewatering pipes. Use Dish structure is a powerful ... more details
Image anion2.png thumb 150px Keggin structure Image anion4.png thumb 150px Keggin structure Keggin structure ... 662 ref The structure self assembles in acidic aqueous solution and is the most stable structure ... by J ns Jakob Berzelius Berzelius in 1826. In 1892, Blomstrand proposed the structure of phosphomolybdic ... compound s ideas of Copaux, attempted to explain the structure of silicotungstic acid . He ... group by secondary valences. This proposal accounted for the characteristics of most poly acids, but not all. In 1928, Linus Pauling proposed a structure for Keggin anions consisting of a tetrahedral ... sub 6 sub octahedral. In this proposed structure, three of the oxygen on each of the octahedral molecular ... . This structure explained many characteristics that were observed such as basicities of alkali metal salts and the hydrated of some of the salts. However the structure could not explain the structure ... the structure of Keggin anions in 1934. The Keggin structure accounts for both the hydrated and dehydrated Keggin anions without a need for significant structural change. The Keggin structure is the widely accepted structure for the Keggin anions. ref J.C. Bailar, Jr. The Chemistry of the Coordination Compounds, Reinhold Publishing Corporation, 1956, pp 472 482 ref Structure and physical properties Image Kegginstructure.jpg 200px Keggin structure of phosphotungstate anion Image KegginCAGE.jpg 200px Cage of the Keggin structure Image Heteroatom.jpg 100px Central tetrahedron The structure ... M sub 3 sub O sub 13 sub units, giving the complete structure an overall tetrahedral symmetry. The bond ... ref G.M. Brown M.R. Noe Spirlet W.R. Bursing H.A. Levy. Acta. Cryst. B33, 1038 1046 1977 ref This structure ... structure there are 5 isomer s, designated by the prefixes , , , and . The original Keggin structure is designated . These isomers are sometimes termed Baker, Baker Figgis or rotational ... the symmetry of the overall structure. Lacunary Keggin structures The term lacunary is applied ... more details
A complex structure may refer to Almost complex manifold Complex manifold Linear complex structure Complex data structure See also Real structure disambig Category Linear algebra ... more details
Refimprove date July 2006 Urban structure is the arrangement of land use in urban areas. Sociologist s, economist s, and geographer s have developed several models, explaining where different types of people and businesses tend to exist within the urban setting. Three models are described in this article. Urban structure can also refer to the Urban spatial structure urban spatial structure , which concerns the arrangement of public and private space in cities and the degree of connectivity and accessibility. Grid model main Grid plan The grid plan, grid street plan or gridiron plan is a type of city plan in which streets run at right angles to each other, forming a grid. In the context of the culture of Ancient Greece , the grid plan is called Hippodamian plan. Zonal model main Concentric ring model This model was the first to explain distribution of social groups within urban areas. Based on one single city, Chicago , it was created by sociologist Ernest Burgess ref Burgess E.W. 1924 The growth .... Sectoral model main Sector model A second theory of urban structure was proposed in 1939 by an economist named Homer Hoyt . ref Hoyt H 1939 The structure and growth of residential neighborhoods in American ... used in United Kingdom Britain and Canada . Secondary Central business district in big cities or Metropolis , Secondary Central business districts develop alongside the Central business district. Industrial ... space in land use planning. Road structure The arrangement of streets and large thoroughfares in cities can be further divided into various arrangements throughout the different regions of the world. The structure .... Roads and Streets are used as a Skeleton of the city. Europe A ringed weblike structure is typically ... nucleus structure and the grid structure. In Southwestern cities such as Phoenix, Arizona Phoenix , this grid structure is astoundingly apparent in http maps.google.com maps?f q&hl en&geocode &time ... photographs of the urban area. References references DEFAULTSORT Urban Structure Category Urban geography ... more details
Dramatic structure is the structure of a drama tic work such as a Play theatre play or film . Many scholars have analyzed dramatic structure, beginning with Aristotle in his Poetics Aristotle Poetics c. 335 BC . This article focuses primarily on Gustav Freytag s analysis of Theatre of ancient Greece ancient Greek and Shakespeare s plays Shakespearean drama. History In his Poetics Aristotle Poetics the Ancient Greece Greek philosopher Aristotle put forth the idea that 1450b27 A whole is what has a beginning and middle and end 1450b27 . ref name fall2 Perseus Digital Library 2006 . http www.perseus.tufts.edu cgi bin ptext?lookup Aristot. Poet. 1450b Aristotle, Poetics ref This three part view of a plot structure with a beginning, middle, and end technically, the protasis , epitasis , and Catastrophe drama catastrophe prevailed until the Roman Empire Roman drama critic Horace advocated a 5 act structure in his Ars Poetica Neue minor neu sit ... act structure. In 1863, around the time that playwrights like Henrik Ibsen were abandoning the 5 act structure and experimenting with 3 and 4 act plays, the Germany German playwright and novelist Gustav Freytag wrote Die Technik des Dramas , a definitive study of the 5 act dramatic structure ... structure is based on five act plays, it can be applied sometimes in a modified manner to short ... rising action, the basic internal conflict is complicated by the introduction of related secondary .... Secondary conflicts can include adversaries of lesser importance than the story s antagonist, who ... narratives Sonata form Three act structure References reflist External links Wiktionary d nouement ... structure http www.clown enfant.com leclown eng drama additions.htm Threeactstructure What s Right With The Three Act Structure by Yves Lavandier , author of Writing Drama Diagrams of Freytag s Pyramid ... Dramatic Structure Category Fiction Category Plot narrative Category Narratology de Dramentheorie ... more details
wiktionary structure The structure of a thing is how the parts of it relate to each other, how it is assembled . Structure may also refer to Architectural structure , a man made structure used or intended for supporting or sheltering any use or continuous occupancy Building , Non building structure & Building disambiguation Canopy ecology structure, organization or three dimensional geometry of a plant canopy Community ecology structure, ecological organization of a biological community Chemical structure , the spatial arrangement of atoms and bonds in a molecule Protein structure Crystal structure , structure of liquids and glasses , the spatial arrangement of ions, atoms, or molecules in condensed matter Data structure , a way of storing data in a computer so that it can be used efficiently Mathematical structure on a set, additional mathematical objects that in some manner attach to the set, making it easier to visualize or work with, or endowing the collection with meaning or significance Structure mathematical logic Algebraic structure Social structure , a pattern of relations Structure and agency , two confronted theories about human behaviour Structural geology , the three dimensional distribution of rock bodies and their planar or folded surfaces, and their internal fabrics Deep structure logical language structure in linguistics The Structure of Scientific Revolutions , a book by Thomas Kuhn on the history of science Structure journal , a scientific journal describing protein structure s Large scale structure of the cosmos Capital structure Financial structure , a cocept within structured finance Structure, the former name for the Express Men clothing brand Structures Structures Boulez , composition Structures album , by John Digweed Structures from Silence , album by Steve Roach Structures of Death , album by Fleshcrawl See also Struct disambiguation disambig ar br Framm da Struktur flertydig fr Structure gl Estrutura it Struttura hu Strukt ra egy rtelm s t ... more details
Cell structure may refer to An organelle , or the layout of organelles of the biological cell itself The structure of a covert cell , often involved in underground resistance, organised crime, terrorism or any group requiring stealth in its operations In mathematics, the structure of a cell complex disambig ... more details
Organic structure may refer to Organic model , forms, methods and patterns found in living systems, often used as a metaphor for non living things The Organic chemistry Molecular structure of an organic compound molecular structure of an organic compound , also known as the structural formula of an organic compound See also Organic disambiguation disambig ... more details
unreferenced date June 2009 bot yes An abstract structure in mathematics is a formal object that is defined by a set of laws, properties, and relationships in a way that is logically if not always historically independent of the structure of contingent experiences, for example, those involving physical objects. Abstract structures are studied not only in logic and mathematics but in the fields that apply them, as computer science , and in the studies that reflect on them, as philosophy and especially the philosophy of mathematics . Indeed, modern mathematics has been defined in a very general sense as the study of abstract structures by the Nicolas Bourbaki Bourbaki group see discussion there, at algebraic structure and also structure category theory structure . An abstract structure may be represented perhaps with some degree of approximation by one or more physical objects this is called an implementation or instantiation of the abstract structure. But the abstract structure itself is defined in a way that is not dependent on the properties of any particular implementation. An abstract structure has a richer structure than a concept or an idea . An abstract structure must include precise rules of behaviour which can be used to determine whether a candidate implementation actually matches the abstract structure in question. Thus we may debate how well a particular government fits ... is or is not a valid game of chess. Examples A sorting algorithm is an abstract structure, but a recipe ... is an abstract structure, but an orchestration is not, because it depends on the properties of particular instruments. Euclidean geometry is an abstract structure, but the theory of continental drift is not, because it depends on the geology of the Earth . A formal language is an abstract structure ... Formal science s Mathematical structure math stub Category Abstraction Category Mathematical terminology Category Structure da Abstrakt begreb lt Abstrakti strukt ra th tr Soyut yap ... more details
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