Refimprove date March 2009 In molecular biology proteinstructure describes the various levels of organization ... NMR spectroscopy , and dual polarisation interferometry to determine the structure of proteins. Protein ... are called conformational change s. Levels of proteinstructure File Main proteinstructure levels en.svg thumb left 250px Proteinstructure , from primary to quaternary structure. There are four distinct levels of proteinstructure. Primary structure Main Protein primary structure The primary structure ... where the amino group is not involved in a peptide bond. The primary structure of a protein is determined .... The sequence of a protein is unique to that protein, and defines the structure and function ... doi 10.1002 prot.21473 ref Tertiary structure Main Protein tertiary structure Tertiary structure refers to three dimensional structure of a single protein molecule. The alpha helices and beta sheets ... the burial of hydrophobic residues from water , but the structure is stable only when the parts of a protein ... structure Main Protein quaternary structure Quaternary structure is a larger assembly of several protein ... alpha and two beta chains of hemoglobin . Domains, motifs, and folds in proteinstructure File Domain ... domain is an element of the protein s overall structure that is self stabilizing and often ... refer to short segments of protein three dimensional structure or amino acid sequence that were found ... structure from random coil . Proteinstructure determination Around 90 of the protein structures ... large protein complexes such as virus coat proteins and amyloid fibers. Structure classification .... Computational prediction of proteinstructure Main Proteinstructure prediction The generation of a protein sequence is much easier than the determination of a proteinstructure. However, the structure ..., a number of methods for the computational prediction of proteinstructure from its sequence ... methods can build a 3D model for a protein of unknown structure from experimental structures of evolutionary ... more details
see also Sequence database In biology , a proteinstructure database is a database that is data modeling modeled around the various proteinstructureProteinstructure determination experimentally determined proteinstructure s. The aim of most proteinstructuredatabases is to organize and annotate the protein structures, providing the biological community access to the experimental data in a useful way. Data included in proteinstructuredatabases often includes three dimensional coordinates as well ... proteinstructuredatabases Because the PDB releases data into the public domain , the data has been used in various other proteinstructuredatabases. Examples of proteinstructuredatabases include ... instances, in this case either proteins or a specific structure determinations of a protein, also contain sequence information and some databases even provide means for performing sequence based queries, the primary attribute of a structure database is structural information, whereas Sequence database sequence databases focus on sequence information, and contain no structural information for the majority of entries. Proteinstructuredatabases are critical for many efforts in computational biology such as Drug design Structure based structure based drug design , both in developing the computational ... about the function of a protein. The Protein Data Bank main Protein Data Bank The Protein Data Bank PDB was established in 1971 as the central archive of all experimentally determined proteinstructure ... oca docs oca home.html OCA a browser database for proteinstructure function The OCA ... that display those scenes in Jmol. http www.proteinlounge.com ProteinLounge a proteindatabases that includes visuals of proteinstructure. Also, includes protein pathways and gene sequences including ... TOPSAN the Open ProteinStructure Annotation Network &mdash a wiki designed to collect, share and distribute ... Protein Data Bank wwPDB . The mission of the wwPDB is to maintain a single archive of macromolecular ... more details
In biochemistry and molecular biology , the tertiary structure of a protein or any other macromolecule is its three dimensional structure, as defined by the atomic coordinates. ref GoldBookRef title tertiary structure file T06282 ref Relationship to primary structure Tertiary structure is considered to be largely determined by the protein s primary structure the sequence of amino acid s of which it is composed. Efforts to predict tertiary structure from the primary structure are known generally as proteinstructure prediction . However, the environment in which a protein is synthesized and allowed ... to be predicted and sequences of known structure in the Protein Data Bank and thus account for environment ... home. ref name foldhome Determinants of tertiary structure main Protein folding In globular ... Proteinstructure determination The majority of protein structures known to date have been solved ..., and since structure determination is relatively difficult, proteinstructure prediction has been a long standing problem. The first predicted structure of globular protein s was the cyclol ... Quaternary structure Structural biology Protein contact map Protein Contact Map Proteopedia , a collaborative ... protein bioinformatics http predictioncenter.gc.ucdavis.edu Center.html Critical Assessment of Structure ... www.cathdb.info CATH ProteinStructure Classification http ekhidna.biocenter.helsinki.fi dali start ... Home Page a website for community annotation of PDB structures. Protein tertiary structure Biomolecular structure DEFAULTSORT Tertiary Structure Category ProteinstructureProteinstructure 3 Category ... existing algorithm is yet able to consistently predict a proteins tertiary or quaternary structure given only its primary structure learning how to accurately predict the tertiary and quaternary structure of any protein given only its amino acid sequence and the pertinent cellular conditions would ... one stable configuration protein aggregation diseases such as Alzheimer s Disease and Huntington ... more details
Proteinstructure prediction is the prediction of the three dimensional structure of a protein from its amino acid sequence that is, the prediction of its Protein secondary structure secondary , Protein tertiary structure tertiary , and Protein quaternary structure quaternary structure from its Protein ... problem of protein design . Proteinstructure prediction is one of the most important goals pursued ... Structure Prediction . Proteinstructure and terminology Proteins are chains of amino acids ... in the proteinstructure. The 20 amino acids can be classified according to the chemistry of the side ... not have a side chain and therefore can increase the local flexibility in the proteinstructure ... stabilizing the whole structure. The proteinstructure can be considered as a sequence of secondary ... different protein sequences from different evolutionary origins may fold into a similar structure ... side groups within the tertiary three dimensional or quaternary protein subunit structure that can ... databases, the known protein structures have been classified into hierarchical levels of structural ... structures. 16.Primary structure refers to the linear amino acid sequence of a protein, which chemically ... fit poorly at sequential positions in a known proteinstructure. Profile columns represent sequential ... score provides an indication as to whether or not the target protein might adopt such a structure. 19.Quaternary structure is the three dimensional configuration of a protein molecule comprising several ... the local secondary structure s of protein s and RNA sequences based only on knowledge of their primary ... to the X ray crystallography crystal structure of the protein for nucleic acids, it may be determined ... this high accuracy allows the use of the predictions in fold recognition and ab initio proteinstructure ... of current protein secondary structure prediction methods is assessed in weekly Benchmark ... AV year 1965 title Influence of Amino Acid Sequence on ProteinStructure journal Biophys. J. pmid 5884309 ... more details
In biochemistry , quaternary structure is the arrangement of multiple protein folding folded protein or coiling protein molecules in a multi subunit complex. Description and examples Many proteins are actually ... are known as protein subunit s. In addition to the tertiary structure of the subunits, multiple subunit nowiki proteins nowiki possess a quaternary structure , which is the arrangement into which the subunits ... complexes also possess quaternary structure. Examples include nucleosome s and microtubule s. Changes in quaternary structure can occur through Protein conformation conformational changes within individual ... complexes before dissociating into monomers. Determination of quaternary structureProtein quaternary structure can be determined using a variety of experimental techniques that require a sample of protein ..., refs. ref Chou, Kuo Chen Chou & Yu Dong Cai 2003 Predicting protein quaternary structure by pseudo ... SH2 domains or proline rich segments SH3 domains . See also Protein primary structureProtein secondary structureProtein tertiary structure Structural biology References reflist External links http ... EBI &mdash Serves a list of the Probable Quaternary Structure PQS for every protein in the Protein ... proteinprotein interfaces in crystal structures of homologous proteins. Protein quaternary structure Biomolecular structure Category ProteinstructureProteinstructure 4 Category Stereochemistry ... subunit. Examples of proteins with quaternary structure include hemoglobin , DNA polymerase ... a classical approach to biochemistry, established at times when the distinction between a protein and a functional, proteinaceous unit was difficult to elucidate. More recently, people refer to proteinprotein interaction when discussing quaternary structure of proteins and consider all assemblies of proteins as protein complex es. Nomenclature of quaternary structures The number of subunits ... by meric. border 1 valign top 1 monomer 2 protein dimer dimer 3 protein trimer trimer 4 tetramer protein ... more details
Image Myoglobin.png thumb 200px A representation of the 3D structure of the myoglobin protein. alpha ... Protein Data Bank file format PDB file. The rough secondary structure content of a biopolymer ... spectrum. Secondary structure was introduced by Kaj Ulrik Linderstr m Lang at Stanford in 1952. Protein ... methods for defining protein secondary structure e.g. DEFINE, ref cite journal title Identification of structural motifs from protein coordinate data secondary structure and first level supersecondary ... based protein secondary structure assignment journal Proteins year 1995 volume 23 number 4 pages ... biochem tutorials prottute helices.htm title Interactive ProteinStructure Tutorial author ... states The Dictionary of Protein Secondary Structure, in short DSSP, is commonly used to describe the protein secondary structure with single letter codes. The secondary structure is assigned based ... protein secondary structure assignment categories exist sharp turns, Omega loops etc. , but they are less ... structure is that of DSSP protein DSSP , which is a purely electrostatic model. It assigns charges ... accepted as a tool for defining secondary structure. Protein secondary structure prediction See also proteinstructure prediction Predicting protein tertiary structure from only its amino acid sequence is a very challenging problem see proteinstructure prediction , but using the simpler secondary ... protein adopts helical structure, rather than random coil. Several types of methods ... of tertiary structure , in all but the simplest proteinstructure prediction homology ... by secondary structure. See also Folding chemistry protein primary structureprotein tertiary structureprotein quaternary structure translation biology translation structural motif References references Further reading C Branden and J Tooze 1999 . Introduction to ProteinStructure 2nd ed. Garland ... for protein secondary structure prediction Protein secondary structure Biomolecular structure Category ... more details
Image PSI Logo.png thumb right PSI logo The ProteinStructure Initiative PSI is an ongoing effort begun ... function. ref name PSIReport 2007 cite web title Report of the ProteinStructure Initiative Assessment ... and maintaining high throughput structural genomics pipelines, developing computational proteinstructure ... of high throughput structure determination, solving unique protein structures, and preparing for a subsequent production phase. ref name PSI 1 cite web title ProteinStructure Initiative Pilot Phase Fact Sheet publisher ProteinStructure Initiative accessdate October 12, 2008 url http www.nigms.nih.gov ... cite web title ProteinStructure Initiative Production Phase Fact Sheet publisher ProteinStructure ... and biomedical problems. ref name PSI Biology cite web title ProteinStructure Initiative Biology publisher ProteinStructure Initiative accessdate October 12, 2008 url http www.nigms.nih.gov Research FeaturedPrograms PSI psi biology ref Phase 1 The first phase of the ProteinStructure Initiative ... journal author Adams M, Joachimiak A, Kim R et al. title 2003 NIH ProteinStructure Initiative Workshop ... The second phase of the ProteinStructure Initiative PSI 2 lasted from July 2005 to June 2010. Its goal ..., the ProteinStructure Initiative had solved over 4,800 protein structures over 4,100 of these were ... Structure Initiative into the Protein Data Bank The number of sponsored research centers grew ... Consortium on Membrane ProteinStructure NYCOMPS . Two homology modeling centers, the Joint Center ... Structure Initiative Structural Biology Knowledgebase SBKB publisher ProteinStructure Initiative ..., metrics on overall progress, and updates on structure determination technology. Like the Protein ... of Dr. Joshua LaBaer, ref cite web title ProteinStructure Initiative Launches New Resources for the Scientific ... includes centers for high throughput structure determination, centers for membrane protein ... Biology Funding Opportunities cite web title ProteinStructure Initiative Biology Funding Opportunities ... more details
No footnotes date June 2010 Graphical model s have become powerful frameworks for proteinstructure prediction , proteinprotein interaction and Thermodynamic free energy free energy calculations for protein structures. Using a graphical model to represent the proteinstructure allows the solution of many problems including secondary structure prediction, proteinprotein interactions, protein drug interaction, and free energy calculations. There are two main approaches to use graphical models in proteinstructure modeling. The first approach uses discrete variables for representing coordinates or dihedral angle s of the proteinstructure. The variables are originally all continuous values and, to transform ... for proteinstructure Markov random field s, also known as undirected graphical models are common representations ... Let X X sub b sub , X sub s sub be the random variables representing the entire proteinstructure. X ... all other angles in the protein. To extract this structure, researchers use a distance threshold ... constant . Using a PDB file, this model can be built over the proteinstructure. From this model free ... Graphical Models For ProteinStructure Category Graphical models Category Protein methods Category Computational ..., by a sequence of bond length s and dihedral angle s. The probability of a particular Proteinstructure conformation x can then be written as math p X x Theta p X b x b p X s x s X b, Theta ..., and the problem is then transformed to a side chain placement problem. The structure of the graph is also encoded in math Theta math . This structure shows which two variables are conditionally ... graphical models for protein structures Graphical models can still be used when the variables ... models of protein structures Gaussian graphical models are multivariate probability distributions ... of each other. To learn the graph structure as a multivariate Gaussian graphical model, we can use ... a graph structure and the edge strength of the connected nodes. An edge strength corresponds to the potential ... more details
File Protein primary structure.svg thumb 250px A protein primary structure is a chain of amino acid s. The primary structure of peptides and proteins refers to amino acid sequence the linear sequence of its amino acid Structural unit structural units . The term primary structure was first coined by Kaj Ulrik Linderstr m Lang Linderstr m Lang in 1951. By convention, the primary structure of a protein is reported starting from the amino terminal N end to the carboxyl terminal C end. Primary structure ... in the Hedgehog protein autoprocessing. History of protein primary structure The proposal that proteins ... , but nucleic acid and protein folding are so complex that knowing the primary structure often doesn ... , Adv. Protein Chem. , 7 , 1 67. Fruton JS. 1979 Early theories of proteinstructure , Ann .... ISBN 0 387 52830 X Protein primary structure Biomolecular structure Category ProteinstructureProteinstructure 1 Category Stereochemistry ca Estructura prim ria de les prote nes de Prim rstruktur ... polymers, so their primary structure can often be specified by the sequence of amino acid s along ... structure also requires specifying the cross linking atoms, e.g., specifying the cysteine s involved in the protein s disulfide bonds. Other crosslinks include desmosine... The chiral centers ..., which cannot be cleaved by most protease s. Finally, the protein can undergo a variety of posttranslational ... . methylation Several protein residues can be methylated, most notably the positive groups of lysine ... diphtheriae and Bordetella pertussis . Ubiquitin ubiquitination and SUMO protein SUMOylation ... that the ubiquitin tagged protein should be degraded. Most of the polypeptide modifications listed above occur post translationally , i.e., after the protein has been synthesized on the ribosome , typically ... in biological systems. Modifications of primary structure In addition to those listed above, the most important modification of primary structure is peptide cleavage See Protease . Proteins ... more details
Multiple issues context July 2009 refimprove July 2009 This list of software for proteinstructure visualization is a compilation of bioinformatics software used to view proteinstructure s. Such tools are commonly used in molecular biology , and bioinformatics . border 0 align center style border 1px solid 999 background color FFFFFF align left bgcolor CCCCCC NAME Link Author BioBlender http www.bioblender.eu BioBlender official web site SciVis team Visual Molecular Dynamics http www.ks.uiuc.edu Research vmd VMD official website Jmol http www.jmol.org Jmol official web site Jmol development team Geneious Geneious Pro implemented Jmol viewer as part of an all in one sequence analysis software package http www.geneious.com Geneious homepage Geneious development team PyMOL http www.pymolwiki.org index.php Main Page PyMOL Wiki Warren Lyford DeLano RasMol http www.rasmol.org Official website Roger Sayle UCSF Chimera http www.rbvi.ucsf.edu chimera Official website UCSF RBVI STING http www.cbi.cnptia.embrapa.br SMS STAR STING Friend http ilyinlab.org friend Valentin Ilyin http www.molsystems.com vp3ds.html VisProt3DS 3D Stereoscopic view anaglyth, side by side, hardware http www.molsystems.com vp3ds.html Official website Nick Vtyurin http polyview.cchmc.org polyview3d.html Polyview 3D Web based high resolution static views and animations using Pymol or Rasmol http polyview.cchmc.org polyview3d.html Official website Aleksey Porollo & Jarek Meller See also Biological data visualization List of molecular graphics systems List of Open Source Bioinformatics software List of software for molecular mechanics modeling List of nucleic acid simulation software Molecular graphics Category Bioinformatics Category Lists of software ProteinStructure Category Bioinformatics software science software stub ... more details
infobox biodatabase title TOPSAN logo File Database.png description collaborative annotation environment for structural genomics. scope organism center Sanford Burnham Medical Research Institute laboratory Joint Center for Structural Genomics author Dana Weekes pmid Weekes & al. 2010 ref name pmid20716366 released 2010 standard format url http www.topsan.org. download webservice sql sparql webapp standalone license versioning frequency curation bookmark version The Open Protein Structure Annotation Network TOPSAN is a wiki designed to collect, share and distribute information about Protein structure protein three dimensional structures ref name pmid20716366 cite journal quotes yes last Weekes first Dana authorlink coauthors Krishna S Sri, Bakolitsa Constantina, Wilson Ian A, Godzik Adam, Wooley John year 2010 month title TOPSAN a collaborative annotation environment for structural genomics journal BMC Bioinformatics volume 11 issue pages 426 publisher location England issn pmid 20716366 doi 10.1186 1471 2105 11 426 bibcode oclc id url pmc 2936398 language eng format accessdate laysummary laysource laydate quote ref References references See also protein structure External links http www.topsan.org. Biodatabase stub Category Biological databases Category Protein structure Category Wikis ... more details
In computational biology , de novo proteinstructure prediction is the task of estimating a protein s tertiary structure from its primary structure sequence alone. The problem is very difficult and has occupied leading scientists for decades. Research has focused in three areas alternate lower resolution representations of proteins, accurate energy functions, and efficient sampling methods. At present, the most successful methods have a reasonable probability of predicting the fold of a small protein domain within 5 angstrom s. Citation needed date November 2008 ref name pande 2002 De novo proteinstructure prediction methods attempt to predict tertiary structures from sequences based on general principles that govern protein folding energetics and or statistical tendencies of conformational features that native structures acquire, without the use of explicit protein threading templates . A general paradigm for de novo prediction involves sampling Configuration space conformation space .... To predict proteinstructure de novo for larger proteins will require better algorithms and larger ..., the potential benefits of structural genomics by predicted or experimental methods make de novo structure prediction an active research field. See also Proteinstructure prediction Proteinstructure prediction software Protein design References Reflist refs ref name samudrala 1998a Samudrala R, Moult J. An all atom distance dependent conditional probability discriminatory function for proteinstructure ... & Baker, D. 2001 . Ab Initio ProteinStructure Prediction Progress and Prospects. Annu. Rev. Biophys ... Foldit http fold.it portal Category Bioinformatics Category Proteinstructure Category Protein methods protein stub bioinformatics stub ... of the properties of native protein conformations ref name samudrala 1998a . De novo methods tend ... Pande, Baker, et.al. Atomistic protein folding simulations on the hundreds of microsecond timescale ... more details
This list of proteinstructure prediction software summarizes commonly used software tools in proteinstructure prediction , including homology modeling , protein threading , ab initio methods, Proteinstructure prediction Secondary structure secondary structure prediction , and transmembrane helix and signal ... phyre server Protinfo CM Comparative modelling of proteinstructure using minimum perturbation and loop ... main article De novo proteinstructure prediction class wikitable style text align center Name ... fragement structure reassembly On line server for protein modeling http zhanglab.ccmb.med.umich.edu ... bioserv.rpbs.univ paris diderot.fr PEP FOLD Server Secondary structure prediction main article Protein ... structure prediction software Category Lists of software Category Protein methods Category Protein ... urbm bioinfo esypred server FoldX Energy calculations and protein design Downloadable program ... http robetta.org server BHAGEERATH H Combination of ab initio folding and homology methods Protein tertiary structure predictions http www.scfbio iitd.res.in bhageerath bhageerath h.jsp server Selvita Protein Modeling Platform Package of tools for protein modeling Free demo, interactive webserver and standalone program including BLAST search, CABS modeling, 3D threading, Psi Pred secondary structure prediction http www.selvita.com selvita protein modeling platform.html Home page SWISS MODEL Local ... servers html index.html Webinterface Threading fold recognition main article Protein threading class wikitable style text align center Name Method Description Link RaptorX software for protein ... structure Webserver http bioinf.cs.ucl.ac.uk psipred main page MUSTER profile profile alignment Webserver ... download br http ttic.uchicago.edu jinbo articles Selvita Protein Modeling Platform Package of tools for protein modeling Free demo, interactive webserver and standalone program including 3D threading and flexible 3d threading http www.selvita.com selvita protein modeling platform.html Home page ... more details
PBB geneid 6749 Structure specific recognition protein 1 , also known as SSRP1 , is a human protein. ref name entrez cite web title Entrez Gene SSRP1 structure specific recognition protein 1 url http www.ncbi.nlm.nih.gov sites entrez?Db gene&Cmd ShowDetailView&TermToSearch 6749 accessdate ref The PBB Summary template is automatically maintained by Protein Box Bot. See Template PBB Controls to Stop updates. PBB Summary section title summary text The protein encoded by this gene is a subunit of a heterodimer that, along with SUPT16H, forms chromatin transcriptional elongation factor FACT biology .... This encoded protein contains a high mobility group box which most likely constitutes the structure recognition element for cisplatin modified DNA. This protein also functions as a co activator of the transcriptional activator p63. ref name entrez Interactions Structure specific recognition protein 1 has been shown to Proteinprotein interaction interact with NEK9 . ref name pmid14660563 cite .... title Nek9, a novel FACT associated protein, modulates interphase progression journal J. Biol. Chem ... group box protein that recognizes structural distortions to DNA caused by binding of the anticancer ..., et al. title Isolation of cDNAs encoding a human protein that binds selectively to DNA modified by the anticancer ... Dyer MA, Hayes PJ, Baron MH title The HMG domain protein SSRP1 PREIIBF is involved in activation ... factor and the high mobility group protein SSRP1. journal J. Biol. Chem. volume 274 issue 22 ... the nuclear high mobility group HMG protein SSRP1 in sera from patients with systemic lupus erythematosus ... pmc 207616 cite journal author Tan BC, Lee SC title Nek9, a novel FACT associated protein, modulates ... doi 10.1074 jbc.M311477200 refend External links MeshName SSRP1 protein, human gene 11 stub NLM ... controls for Protein Box Bot, please see Template PBB Controls for details. PBB Controls update page yes require manual inspection no update protein box yes update summary no update citations yes ... more details
DeZign for Databases is a database design and data modeling tool for multiple database platforms Oracle Database Oracle , MySQL , IBM DB2, PostgreSQL , MS SQL Sever, MS Access, ... . It can be used to create, maintain and document new or existing database systems. The tool uses Entity relationship diagram . Similar tools are Embarcadero ER Studio , IBM Data Architect, Oracle Designer and Sybase PowerDesigner . History DeZign for Databases was created by Heraut Solutions in 1998. Later the company name was changed to Datanamic. DeZign for Databases was the first modeling tool to support MySQL . Support for more databases was added in the late nineties. About 20 databases are supported in the 2008 version of the tool. See also Computer aided software engineering Relational Model Data modeling RDBMS External links http www.datanamic.com dezign Official website http www.datanamic.com support lt dez005 introduction db modeling.html Introduction to database design Category Desktop database application development tools Category Data modeling tools ... more details
saved book title Databases subtitle The Complete Wikipedia Guide cover image cover color Databases Introduction Data management Database Database system Database management system Types of DBMS Data store Technical Information Project Data Modeling Introduction to Data Modeling Data modeling Data model Database model Database design Conceptual schema Data structure diagram Hierarchical database model Network model Navigational database ERD Entity relationship model Has a Many to many data model Enhanced Entity Relationship Model Weak entity Associative Entities Structured Entity Relationship Model Barker s Notation Peter Chen Other Data Modeling Techniques Unified Modeling Language The Third Manifesto Three schema approach White pages schema Anchor Modeling Bachman diagram Bitemporal Modeling Bitemporal data IDEF1X Universal Data Element Framework Terminology model Georelational data model Semantic data model Relational Model Tasmania Relational Schema Relational model Relational database Relational database management system Life cycle of a relational database Logical data model Logical schema Relation database Table database Tuple Row database Attribute domain Candidate key Unique ... language Nonprocedural language Facebook Query Language Technologies Databases Programming Active ... Cursor databases SQL Problems Requiring Cursors WxSQLite3 Database connectivity Application programming ... in Relational Databases Normal Form Data redundancy Database normalization Functional dependency ... Soft error Two pass verification Validation rule Non Relational Databases XML Semi structured data ... Object Database Zope Object Database No SQL Databases NoSQL RDBMS NoSQL Graph database DEX Graph database ... MongoDB Spatiotemporal Databases Temporal database RRDtool Spatial database Spatial query Spatiotemporal ... metadata Geographical database Time series database Operational historian Special Databases Real time ... Mobile Transaction Models Well Known Databases Standard data model Suppliers and Parts database ... more details
Orphan date June 2011 There are a number of databases that psychologists use to access the knowledgebase of their science. They include MEDLINE PubMed PsycINFO PsycARTICLES PsycFIRST PsycSCANs Online PsycSCAN Applied Psychology PsycSCAN Behavior Analysis & Therapy PsycSCAN Developmental Psychology PsycSCAN LD MR PsycSCAN Psychopharmacology Cochrane Library CINAHL EMBASE Psychological Abstracts PsycLit Ulrich International Periodical Directory , PUBLIST The Internet Directory Publications , ISSN International , PSICODOC , PSEDISOC , the ISOC database CSIC RISO , CIRBIC REVISTAS , COMPLUDOC Institute for Scientific Information Thomson ISI Science Citation Index Social Sciences Citation Index Psychology stub Category Psychology lists Category Scientific databases ... more details
analysis application , which incorporates studies from one or more public databases e.g. http www.bioinformatics.ubc.ca ... NextBio uses various sources Some of the most known public, curated microarray databases are In order to keep this list short, please add new databases only if they are discussed in the article ... add your favourite databases to the maintained list at the Open Directory Project, linked below. class ... Databases, see dmoz Science Biology Biochemistry and Molecular Biology Gene Expression Databases Gene Expression Databases See also Biological database DNA microarray DNA microarray Data warehousing genetics stub biology stub Category Microarrays Category Biological databases ... more details
In computer science and technology, a database cursor is a control structure that enables wikt traverse traversal over the database record records in a database. Cursors facilitate subsequent processing in conjunction with the traversal, such as retrieval, addition and removal of database records. The database cursor characteristic of traversal makes cursors akin to the programming language concept of iterator . Cursors are used by database programmers to process individual rows returned by database system queries. Cursors enable manipulation of whole result set s at once a capability that most procedural programming languages lack. In this scenario, a cursor enables the rows in a result set to be processed sequentially. In SQL procedures, a cursor makes it possible to define a result set a set of data rows and perform complex logic on a row by row basis. By using the same mechanics, an SQL procedure can also define a result set and return it directly to the caller of the SQL procedure or to a client application. A cursor can be viewed as a pointer to one row in a set of rows. The cursor can only reference one row at a time, but can move to other rows of the result set as needed. To use cursors in SQL procedures, you need to do the following Declare a cursor that defines a result set. Open the cursor to establish the result set. Fetch the data into local variables as needed from the cursor, one row at a time. Close the cursor when done. To work with cursors you must use the following SQL statements This section introduces the ways the SQL 2003 standard defines how to use cursors in applications in embedded SQL. Not all application bindings for relational database systems adhere ... , Richard Stones Beginning Databases with PostgreSQL From Novice to Professional , Apress, ISBN ... com.ibm.db2.udb.apdv.sql.doc doc c0024361.htm Cursors in DB2 SQL stored procedures Databases DEFAULTSORT Cursor Databases Category Database management systems Category SQL es Cursor base de datos ... more details
Glass databases are a collection of glass compositions, glass properties, glass model s, associated trademark names, patent s etc. These data were collected from publications in scientific papers and patents, from personal communication with scientists and engineers, and other relevant sources. History Since the beginning of scientific glass research in the 19th century thousands of glass property composition datasets were published. The first attempt to summarize all those data systematically was the monograph Glastechnische Tabellen . ref Glastechnische Tabellen engl. Glass Technical Tables , edited by W. Eitel, M. Pirani, and K. Scheel, Springer Verlag, Berlin, 1932 ref World War II and the Cold War prevented similar efforts for many years afterwards. In 1956 Phase Diagrams for Ceramists was published the first time, containing a collection of phase diagram s. ref Levin, E.M., McMurdie, H.F., and Hall, F.P., Phase Diagrams for Ceramists Volume 1, The American Ceramic Society, Columbus, Ohio, p. 6, 1956. ref This database is known today as Phase Equilibria Diagrams . ref http www.ceramics.org phase Phase Equilibria Diagrams Database ref In 1991 the Japanese database Interglad was created, ref http www.newglass.jp interglad 6 gaiyo info e.html INTERGLAD ref followed by the publication of the Handbook of Glass Data in 1993. ref Handbook of Glass Data , edited by O. V. Mazurin, M. V. Streltsina, and T. P. Shvaiko Shvaikovskaya, Elsevier, 1993 ref The Handbook of Glass Data was later digitalized and substantially expanded under the name SciGlass . ref http www.sciglass.info SciGlass ref Currently, SciGlass contains properties of about 350,000 glass compositions, INTERGLAD about ... features see the references section below. All databases contain citations to the original data sources ... point s, crystalline phases, primary crystalline phase s Application of glass databases Experimental ... Glass chemistry Category Chemical databases Category Ceramic materials ... more details
Dablink This article deals with the term directory with respect to a computer database . The term also commonly refers to a Directory file systems folder in a computer file system . Unreferenced date April 2007 Merge Directory service date September 2009 Generally, a directory , as used in computing and telephony , refers to a digital library repository or database of information which is heavily optimized for reading, under the assumption that data updates are very rare compared to data reads. Commonly, a directory supports search and browsing in addition to simple lookups. A website which offer access to a categorized listing of other websites optimized for lookup, search, or browsing is a directory, a web directory . The Open Directory Project is an example of a web directory. Directory technology is often used in White pages white page applications and network information services. WHOIS is a prominent example of directory service providing white pages. The Domain Name System DNS is a prominent example of directory service providing a network information service. DNS is also an example of a Distributed computing distributed hierarchical directory service that only has simple lookup capabilities. The X.500 and Lightweight Directory Access Protocol LDAP directory services are examples of general purpose distributed hierarchical object oriented directory technologies. Both offer complex searching and browsing capabilities and are used for white pages, network information services, public key infrastructure , and a wide range of other applications. See also Database Directory service Reference works Web directory RSS directory DEFAULTSORT Directory Databases Category Types of databases Category Reference works ... more details
thumb right A representation of the 3D structure of the protein myoglobin showing colored alpha helix alpha helices . This protein was the first to have its structure solved by X ray crystallography ... chains in a protein that ultimately determines its three dimensional structure and its chemical reactivity .... Protein is generally used to refer to the complete biological molecule in a stable tertiary structure ... structure conformation . Synthesis Main Protein biosynthesis Image Ribosome mRNA translation en.svg ... Proteinstructure Further2 Proteinstructure prediction File Chaperonin 1AON.png thumb 300px right The crystal structure of the chaperonin. Chaperonins assist protein folding. File Proteinviews 1tim.png thumb 300px Three possible representations of the three dimensional structure of the protein triose ... distinct aspects of a protein s structure ref Murray et al ., pp. 30 34. ref Primary structure the peptide ... can be present in the same protein molecule. Tertiary structure the overall shape of a single protein ... fold . The tertiary structure is what controls the basic function of the protein. Quaternary structure the structure formed by several protein molecules polypeptide chains , usually called protein ... Discovering the tertiary structure of a protein, or the quaternary structure of its complexes, can provide important clues about how the protein performs its function. Common experimental methods of structure ... by systematically solving representative structures of major fold classes. Proteinstructure prediction ... structure of the protein, which defines the binding site pocket, and by the chemical properties ... directed mutagenesis , researchers can alter the protein sequence and hence its structure, cellular ... prediction and simulation Main proteinstructure prediction List of proteinstructure prediction software Complementary to the field of structural genomics, proteinstructure prediction seeks to develop ... as homology modeling , relies on the existence of a template structure with sequence similarity to the protein ... more details
modifications. European Bioinformatics Institute ProteinstructuredatabasesProtein Data Bank PDB comprising ... CATH ProteinStructure Classification http www.ebi.ac.uk pdbsum PDBsum Proteinstructure prediction Protein model databases http swissmodel.expasy.org SWISS MODEL.html SWISS MODEL Server and Repository for ProteinStructure Models http salilab.org modbase ModBase Database of Comparative ProteinStructure Models Sali Lab, University of California, San Francisco UCSF Protein Model Portal http proteinmodelportal.org PMP Meta database that combines several databases of proteinstructure models ... Information The three databases, DDBJ Japan , GenBank USA and European Nucleotide Archive Europe , are repositories for nucleotide primary structure sequence data from all organism s. All three databases ... Resource Center for Invertebrate Vectors of Human Pathogens Protein sequence databases UniProt ... of snoRNAs Carbohydrate structuredatabases Eurocarbdb EuroCarbDB http www.ebi.ac.uk eurocarb ... protein interactions. European Molecular Biology Laboratory EMBL Signal transduction pathway databases ...Multiple issues cleanup January 2011 external links November 2010 orphan April 2012 Biological databases ... A title Databases, data tombs and dust in the wind. journal Bioinformatics volume 24 issue 19 pages ... databases ref name metabase cite journal author Bolser D.M et al. title MetaBase the wiki database of biological databases journal NAR volume 40 pages D1250 year 2012 url http nar.oxfordjournals.org content early 2011 12 01 nar.gkr1099.abstract ref . Primary nucleotide sequence databases The International ... INSD http www.insdc.org consists of the following databases. http www.ddbj.nig.ac.jp Welcome e.html ... to achieve optimal synchronisation between them. These three databases are primary databases, as they house ... of databases, rather than any one integration project or technology. They collect data from ... http harvester.fzk.de Karlsruhe Institute of Technology Integrating 26 major protein gene resources ... more details
Pfam box Symbol SpA Name Protein A image Protein A 1DEE 1L6X.png width caption Structure of a domain of protein A as a three helix bundle binding to the heavy variable chain of a VH3 human Fab ref name ... JB, Silverman GJ. title Crystal structure of a Staphylococcus aureus protein A domain complexed with the Fab ... month May pmid 10805799 doi pmc 25840 ref left. Minimized protein A bound to Fc fragment of Rituximab ... April pmid 10754313 doi ref Pfam InterPro SMART PROSITE SCOP 1DEE TCDB OPM family OPM protein PDB PDB2 1dee , PDB2 1l6x Protein A is a 56 Atomic mass unit kDa MSCRAMM surface protein originally found ... and phagocytosis . Protein A antibody binding Protein A binds with high affinity to human IgG1 and IgG2 as well as mouse IgG2a and IgG2b. Protein A binds with moderate affinity to human IgM ... or IgD , nor will it react to mouse IgM, IgA or IgE. The capacity of protein A to bind antibodies with such high .... The protein A used for production of antibodies in bio pharmaceuticals is most commonly bound to a stationary phase chromatography resin. Other antibody binding proteins In addition to Protein A, other immunoglobulin binding bacterial proteins such as Protein G , Protein A G and Protein L are all ... Staphylococcus aureus utilizes Protein A, along with a host of other proteins and surface factors to aid its survival and, thus, virulence. Protein A helps inhibit phagocytic engulfment and acts as an immunological disguise. Mutants of S. aureus lacking protein A are more efficiently phagocytosed ... toxin. J. Exp. Med. 2003 197 1125 1139. ref Research Recombinant Staphylococcal Protein ... form of Protein A is called MabSelect. ref http www.gelifesciences.com aptrix upp00919.nsf Content 17D93C2E6A580E57C1257628001CE677 file 18114994AE.pdf ref Protein A is often coupled to other molecules .... Protein A is often immobilized onto a solid support and used as reliable method for purifying total IgG from crude protein mixtures such as blood serum serum or ascites fluid, or coupled with one ... more details
Primary structure of bovine vitamin K dependent protein S journal Proc. Natl. Acad. Sci. U.S.A. volume ...PBB geneid 5627 Protein S is a vitamin K dependent plasma glycoprotein synthesized in the endothelium. In the circulation, Protein S exists in two forms a free form and a complex form bound to complement system complement protein C4b binding protein C4BP . In humans, protein S is encoded by the PROS1 ... B, Stenflo J, Wydro R title Isolation and sequence of the cDNA for human protein S, a regulator ... url ref In 1979, researchers in Seattle , Washington first discovered protein S and arbitrarily ... X Stuart factor , and protein S journal Biochemistry volume 16 issue 4 pages 698 706 year 1977 ... RG, Davie EW title Characterization of protein S, a gamma carboxyglutamic acid containing protein ... March pmid 420821 doi 10.1021 bi00572a026 ref Function The best characterized function of Protein S is its role in the anti coagulation pathway, where it functions as a cofactor to Protein C in the inactivation .... ref name pmid18695379 cite journal author Castoldi E, Hackeng TM title Regulation of coagulation by protein ... 18695379 doi 10.1097 MOH.0b013e328309ec97 url ref Protein S can bind to negatively charged phospholipids via the carboxylated Gla domain GLA domain . This property allows Protein S to function in the removal ... such as macrophages . Protein S can bind to the negatively charged phospholipids and function as a bridging molecule between the apoptotic cell and the phagocyte. The bridging property of Protein ... lead to Protein S deficiency which is a rare blood disorder which can lead to an increased risk of thrombosis ... R, Daly ME title The prevalence of, and molecular defects underlying, inherited protein S deficiency ... author Garc a de Frutos P, Fuentes Prior P, Hurtado B, Sala N title Molecular basis of protein S deficiency ... doi url ref Interactions Protein S has been shown to Proteinprotein interaction interact with Factor ... 621 635 of protein S are essential for binding to factor Va journal J. Biol. Chem. volume 274 issue ... more details
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