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Protein Data Bank





Encyclopedia results for Protein Data Bank

  1. Protein Data Bank

    infobox biodatabase title The Protein Data Bank. logo File Database.png description Protein structure br Crystallography scope organism center laboratory author pmid released standard format Protein Data ... versioning frequency curation bookmark version The Protein Data Bank PDB is a repository for the 3 D structural data of large biological molecules, such as protein s and nucleic acid s. See also crystallographic database . The data, typically obtained by X ray crystallography or Protein NMR NMR ... the Worldwide Protein Data Bank , wwPDB. The PDB is a key resource in areas of structural biology .... M. last Berman year 2008 month January title The Protein Data Bank a historical perspective pmid 18156675 ... Data Bank journal Protein Science volume 6 pages 1591 1597 publisher Cambridge University Press ref ... TN, Weissig H, Shindyalov IN, Bourne PE year 2000 month January title The Protein Data Bank journal ... of the RCSB . ref cite web title RCSB PDB Newsletter Archive publisher RCSB Protein Data Bank ... format The file format initially used by the PDB was called the Protein Data Bank file format PDB ... External links http www.wwpdb.org The Worldwide Protein Data Bank wwPDB &mdash parent site to regional hosts below http www.pdb.org RCSB Protein Data Bank USA http www.pdbe.org PDBe Europe http ... ar ca Protein Data Bank da Protein Data Bank de Protein Data Bank es Protein Data Bank fa fr Protein Data Bank ko it Protein Data Bank he nl Protein Data Bank ja pl Protein Data Bank pt Protein Data Bank ru Protein Data Bank sr Proteinska banka podataka fi Protein Data Bank uk zh ... of protein structure data determined by X ray diffraction and 2 the newly available 1968 molecular graphics ... . The http www.bmrb.wisc.edu BMRB joined in 2006. Each of the four members of Worldwide Protein Data Bank wwPDB can act as deposition, data processing and distribution centers for PDB data. The data ...   more details



  1. Worldwide Protein Data Bank

    The Worldwide Protein Data Bank , wwPDB, is an organization whose mission, according to its website, ref Worldwide Protein Data Bank. URL http www.wwpdb.org http www.wwpdb.org . Accessed on April 22, 2009. ref is to maintain a single Protein Data Bank Archive of macromolecular structural data that is freely and publicly available to the global community. Given the open access publishing open access goal, it is somewhat ironic that the announcement of the collaborative was made in a pay for access scientific journal journal Nature Structual Biology . ref name pmid14634627 cite journal author Berman H, Henrick K, Nakamura H title Announcing the worldwide Protein Data Bank journal Nat. Struct. Biol ... for Structural Bioinformatics Protein Database, http www.rcsb.org pdb RCSB PDB USA Protein Data Bank in Europe, http www.pdbe.org PDBe Protein Data Bank Japan, http www.pdbj.org PDBj Biological Magnetic Resonance Data Bank, http www.bmrb.wisc.edu BMRB USA The wwPDB was founded in 2003 by http ... of the protein data bank archive journal Nucleic Acids Res. volume 36 issue Database issue pages D426 ... PDB protein data bank External links The parent organization http www.wwpdb.org wwPDB The four member ... Protein Databank USA http www.pdbe.org PDBe , Protein Data Bank in Europe http www.pdbj.org PDBj , Protein Data Bank Japan http www.bmrb.wisc.edu BMRB , Biological Magnetic Resonance Data Bank USA ..., K. Nakamura, H. Markley, J. L. year 2007 month January date title The worldwide Protein Data Bank wwPDB ensuring a single, uniform archive of PDB data journal Nucleic Acids Res. volume 35 issue ... &HITS 10&hits 10&RESULTFORMAT &fulltext Protein Data Bank&searchid 1&FIRSTINDEX 0&resourcetype ... data and process the data. The processed data is sent to the archive keeper , which is agreed to be RCSB PDB. This ensures that there is only one version of the data which is identical for all users. The modified ... structure files available through their websites to the public. Data is accessed from the wwPDB ...   more details



  1. Protein Data Bank (file format)

    an interface for Python programming language Python The Protein Data Bank Molecular visualization ... The RCSB Protein Data Bank http www.pdbe.org Protein Data Bank in Europe http www.ncbi.nih.gov Structure ... of the atoms that are part of the protein. For example, the first ATOM line above describes the alpha ... are not part of the protein molecule. SEQRES records give the sequences of the three peptide chains ... NCBI http www.rcsb.org pdb uniformity index.html The Data Uniformity Project from PDB http ... protein stub ko PDB ...   more details



  1. Data bank

    In telecommunication s, a data bank is a repository of information on one or more subjects that is organized in a way that facilitates local or remote information retrieval. A data bank may be either centralized or decentralized. In this sense, data bank is synonym ous with database . Data bank may also refer to an organization primarily concerned with the construction and maintenance of a database . Sources FS1037C MS188 The American Heritage Dictionary of the English Language , Fourth Edition . Houghton Mifflin , 2000. Category Data management telecomm stub el ...   more details



  1. Conformational dynamics data bank

    infobox biodatabase title Conformational dynamics data bank logo File Database.png description conformational dynamics of proteins and supramolecular protein assemblies. scope organism center laboratory author pmid PMID 21051356 released 2010 standard format url http www.cdyn.org download webservice sql sparql webapp standalone license versioning frequency curation bookmark version The conformational dynamics data bank CDDB is a database about conformational dynamics of heavy proteins and protein assemblies. ref cite journal quotes yes last Kim first Do Nyun authorlink coauthors Altschuler Josiah, Strong Campbell, McGill Ga l, Bathe Mark year 2011 month Jan title Conformational dynamics data bank a database for conformational dynamics of proteins and supramolecular protein assemblies journal Nucleic Acids Res. volume 39 issue Database issue pages D451 5 publisher location England issn pmid 21051356 doi 10.1093 nar gkq1088 bibcode oclc id url language eng format accessdate laysummary laysource laydate quote ref References references External links http www.cdyn.org Biodatabase stub Category Biological databases Category Protein structure ...   more details



  1. National Trauma Data Bank

    The National Trauma Data Bank NTDB , also called the American College of Surgeons National Trauma Data Bank , is a compilation of information about Trauma medicine traumatic injuries and outcomes in the United States . Hospital emergency room s and other institutions such as trauma center s which are participants submit data and receive in return access to reports analyzing data about both their own operations and trauma medicine in the United States as a whole. ref name homepage http www.facs.org trauma ntdb index.html Homepage National Trauma Data Bank , accessed October 8, 2010 ref Annual reports, an annual report and a pediatric report, which include demography demographic information is issued. Access to data sets is available to researchers who apply and are approved. ref name homepage ref Notes reflist External links http www.facs.org trauma ntdb index.html Homepage National Trauma Data Bank http www.facs.org trauma ntdb docpub.html NTDB Reports and Publications http www.facs.org trauma ntdb ntdbannualreport2010.pdf 2010 National Trauma Data Bank Annual Report http www.facs.org trauma ntdb ntdbpediatricreport2010.pdf 2010 National Trauma Data Bank Pediatric Report Category Statistical organizations Category Medical emergencies Category Traumatology Category Causes of death Category Healthcare in the United States ...   more details



  1. DNA Data Bank of Japan

    Data Bank of Japan DDBJ entry in MetaBase . Category Genomics Category Molecular biology Category ...   more details



  1. Dortmund Data Bank

    The Dortmund Data Bank ref Onken U., Rarey Nies J., Gmehling J., The Dortmund Data Bank A Computerized ..., 10 3 , 739 747, 1989 ref short DDB is a factual data bank for thermodynamic and thermophysical data. Its main usage is the data supply for process simulation where experimental data are the basis ... .png 250px thumb Double Azeotrope of Benzene and Hexafluorobenzene , taken from Dortmund Data Bank Phase equilibria data vapor liquid equilibrium vapor liquid , liquid liquid extraction liquid liquid , solid liquid , data on Azeotrope azeotropy and zeotropy Mixing Enthalpy Mixing enthalpies Gas ... , benzene, and acetone gallery Data Sources The DDB is a collection of experimental data published by the original authors. All data are referenced and a quite large literature data bank is part .... Secondary sources like data collections are normally neglected and only used as a literature source. Derived data are also not collected with the main exception of the azeotropic data bank which is built partly from evaluated vapor liquid equilibrium data. History The Dortmund Data Bank was founded ... Technical University in Tallinn , and others. Availability The Dortmund Data Bank is distributed by DDBST GmbH as in house software. Many parts of the Dortmund Data Bank are also distributed as part of the DETHERM data bank which is also available online. References references See also Beilstein ... solubilities Octanol Water partition coefficient s Critical point thermodynamics Critical data The mixture data banks contain currently April 2007 approx. 308,000 data sets with 2,157,000 data points ... Thermal conductivities Critical point thermodynamics Critical data Critical temperature T sub ... of sound P v T data including virial coefficient s Energy functions Enthalpy Enthalpies and Entropy entropies Surface tension s The pure component properties data bank contains currently April 2007 approx. 157,000 data sets with 1,080,000 data points for 16700 different components. gallery Image ...   more details



  1. EM Data Bank

    The EM Data Bank or Electron Microscopy Data Bank EMDB collects 3D EM maps and associated experimental data determined using electron microscopy of biological specimens. It was established in 2002 at the http www.ebi.ac.uk pdbe MSD PDBe group of the http www.ebi.ac.uk European Bioinformatics Institute EBI , where the European site of the http www.wwpdb.org wwPDB consortium is located. It provides both the http emdatabank.org deposit.html EMdep deposition interface and the http emdatabank.org search.html EMsearch search tool. Under the http www.emdatabank.org NIH Unified Data Resource for CryoEM , the http www.rcsb.org Research Collaboration for Structural Biology RCSB also acts as a deposition, data processing and distribution center for EMDB data, while the http ncmi.bcm.tmc.edu ncmi National Center for Macromolecular Imaging NCMI is a collaborative partner in providing services and tools concerning the EMDB. EMDB is an archive for three dimensional density maps of all types of biological assemblies, including ribosomes, chaperones, polymerases, multifunctional enzymes and viruses. http viperdb.scripps.edu EMDB Viper EMDB at The Scripps Research Institute Scripps is a separate database for three dimensional EM maps of viruses. References M. Tagari, et al. 2002 . New electron microscopy database and deposition system . Trends Biochem Sci, 27 11 p. 589. PMID 12417136 S. D. Fuller 2003 . Depositing electron microscopy maps . Structure, 11 1 pp. 11 12. PMID 12517335 K. Henrick, R. Newman, M. Tagari, and M. Chagoyen 2003 . EMDep a web based system for the deposition and validation of high resolution electron microscopy macromolecular structural information . J Struct Biol, 144 ... EM Data Bank http emdatabank.org search.html US and UK Search pages Category Electron microscopy ... biology . J Struct Biol, 151 2 pp. 196 207. PMID 16043364 M. Tagari, et al. 2006 . E MSD improving data ... C. Lawson, et al. EMDataBank.org unified data resource for CryoEM . Nucleic Acids Res. 2011 Database ...   more details



  1. Hazardous Substances Data Bank

    The Hazardous Substances Data Bank HSDB is a toxicology database on the United States U.S. National Library of Medicine s NLM Toxicology Data Network TOXNET . ref http toxnet.nlm.nih.gov Toxnet.nlm.nih.gov ref It focuses on the toxicology of potentially hazardous chemicals, and includes information on human exposure, industrial hygiene , emergency handling procedures, environmental fate, regulatory requirements, and related areas. All data are referenced and derived from a core set of books, government documents, technical reports, and selected primary journal literature. All entries are peer reviewed by a Scientific Review Panel SRP , members of which represent a spectrum of professions and interests. The HSDB is organized into individual chemical records, and contains over 6000 such records. It is accessible free of charge via TOXNET. Users can search by chemical or other name, chemical name fragment, CAS registry number and or subject terms. Recent additions include radioactive materials and certain mixtures, like crude oil and oil dispersants. References references citation title Fact Sheet Hazardous Substances Data Bank HSDB url http www.nlm.nih.gov pubs factsheets hsdbfs.html publisher National Library of Medicine date September 2006 accessdate 2009 08 29 . External links http toxnet.nlm.nih.gov cgi bin sis htmlgen?HSDB HSDB search http toxnet.nlm.nih.gov TOXNET http toxnet.nlm.nih.gov cgi bin sis search r?dbs hsdb term na permethrin 5D HSDB Sample Record Category Chemical safety Category Toxicology Category Chemical databases med toxic stub ...   more details



  1. Video Data Bank

    Video Data Bank VDB is an international video art distribution organization and a resource in the United States for videos by and about contemporary artists. Located in Chicago, Illinois VDB was founded at the School of the Art Institute of Chicago in 1976 at the inception of the media arts movement. VDB provides experimental video art, documentaries made by artists, and taped interviews with visual artists and critics for a wide range of audiences. These include micro cinemas, film festivals, media arts centers, universities, libraries, museums, community based workshops, public television, and cable access centers. Video Data Bank currently holds over 2,000 titles in distribution, by more than 400 artists, available in a variety of screening and archival video formats. It also actively publishes anthologies and curated programs of video art. The preservation of historic video is an ongoing project of the Video Data Bank. The total holdings, including works both in and out of distribution, include over 5,000 titles of original and in some cases, rarely seen, video art and documentaries from the late 1960s on. The VDB functions as a Department of the Art Institute of Chicago and is supported in part by awards from the National Endowment for the Arts and the Illinois Arts Council . History In 1974, VDB co founders Kate Horsfield and Lyn Blumenthal, graduate students at the School ... and Blumenthal officially founded the Video Data Bank, taking over a small collection of student ... the National Alliance for Media Arts and Culture NAMAC named Video Data Bank as the year s Outstanding Media Arts Organization Collections The Video Data Bank maintains three collections of video produced ... 2006 title Feedback The Video Data Bank Catalog of Video Art and Artist Interviews publisher Temple ... http www.vdb.org Video Data Bank http www.moma.org exhibitions film exhibitions.php?id 4551 Feedback The Video Data Bank, Video Art, and Artist Interviews Reprised, Film Exhibition May 17 31, 2007 ...   more details



  1. Cambodia National and Provincial Resources Data Bank

    The Cambodia National and Provincial Resources Data Bank is an online collection of data about Cambodia . It was prepared by the Cambodian Ministry of Commerce with funding from the World Bank and is designed to be accessible to entrepreneurs and investors. ref name greeting Cham Prasidh. http www.moc.gov.kh national data resource Foreword 208.html Message from the Minister . Cambodia National and Provincial Resources Data Bank December 12, 2003 . ref ref name adb http www.adb.org Documents Reports PSA CAM PSA CAM.pdf Private Sector Assessment for the Kingdom of Cambodia . Development Consulting International, for the Asian Development Bank December 2003 . ref It includes information related to human resources, education, business, tourism, culture, environment, geology, infrastructure, transport, international trade, agriculture, investment, and geography. ref name adb References reflist External links http www.moc.gov.kh national data resource ContextN.html Cambodia National and Provincial Resources Data Bank home page Cambodia stub Category Cambodian websites ...   more details



  1. Protein

    in the Protein Data Bank PDB , a freely available resource from which structural data about thousands .... ref name Citation needed date May 2010 As of 2009, the Protein Data Bank has over 55,000 atomic resolution structures of proteins. ref name urlRCSB Protein Data Bank In more recent times ...About a class of molecules protein as a nutrient Protein nutrient other uses pp semi indef pp move indef File Myoglobin.png thumb right 250px 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 ... compound compounds consisting of one or more polypeptide s typically folded into a globular protein globular or fibrous protein fibrous form in a biologically functional way. A polypeptide is a single ... acids in a protein is defined by the DNA sequence sequence of a gene , which is encoded in the genetic ... or even during synthesis, the residues in a protein are often chemically modified by post translational ... together to achieve a particular function, and they often associate to form stable protein complex complex ... to be single structure. Other proteins undergo large rearrangements from one protein conformation ... signaling event . Thus, the structure of a protein serves as a medium through which to regulate either the function of a protein or activity of an enzyme. Not all proteins requiring a folding process ... ingested protein into free amino acids that are then used in metabolism. Proteins were first described ... Jakob Berzelius in 1838. Early nutritional scientists such as the German Carl von Voit believed that protein ... urease was in fact a protein. ref name Sumner1926 The first protein to be protein sequencing .... The first protein structure s to be solved were hemoglobin and myoglobin , by Max Perutz and John ... may be protein purification purified from other cellular components using a variety of techniques such as ultracentrifugation .... Methods commonly used to study protein structure and function include immunohistochemistry , site ...   more details



  1. Protein A

    Protein A is a 40 60 Atomic mass unit kDa MSCRAMM surface protein originally found in the cell wall of the bacteria Staphylococcus aureus . It is encoded by the spa gene and its regulation is controlled by DNA topology, cellular osmolarity, and a two component regulatory system two component system called ArlS ArlR. It has found use in biochemical research because of its ability to bind immunoglobulins . It binds proteins from many of mammalian species, most notably IgG s. It binds with the Fc region ... antibody function on their surface which disrupts opsonization and phagocytosis . Protein A antibody .... Protein A binds with moderate affinity to human IgM , IgA and IgE as well as to mouse IgG3 and IgG1 .... 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 commonly used to purify, immobilize or detect immunoglobulins. Role in pathogenesis As a pathogen Staphylococcus aureus utilizes Protein .... Protein A helps inhibit phagocytic engulfment and acts as an immunological disguise. Mutants of S. aureus lacking protein A are more efficiently phagocytosed in vitro, and mutants in infection models ... 197 1125 1139. ref Research Recombinant Staphylococcal Protein A is often produced in E. coli for use in immunology and other biological research. One recombinant form of Protein A is called MabSelect ... 18114994AE.pdf ref . Protein A is often coupled to other molecules such as a fluorescent dye , enzyme ... widely utilized coupled to magnetic, latex and agarose beads. Protein A is often immobilized onto a solid support and used as reliable method for purifying total IgG from crude protein mixtures ... of antibodies. Immunoprecipitation studies with protein A conjugated to beads are also commonly used to purify proteins or protein complexes indirectly through antibodies against the protein or protein complex of interest. References reflist Category Proteins Category Staphylococcaceae de Protein ...   more details



  1. Protein S

    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. In humans, protein S is encoded by the PROS1 gene . ref name pmid2944113 ... J, Wydro R title Isolation and sequence of the cDNA for human protein S, a regulator of blood coagulation ... in Seattle, Wash, first discovered protein S and arbitrarily named it after the city of its ... title A comparison of human prothrombin, factor IX Christmas factor , factor X Stuart factor , and protein ... of protein S, a gamma carboxyglutamic acid containing protein from bovine and human plasma ... 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 of factor V Factors ... journal author Castoldi E, Hackeng TM title Regulation of coagulation by protein S journal Curr. Opin ... 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 of cells which are undergoing ... membrane. These negatively charged phospholipids are recognized by phagocytes such as macrophages . Protein ... the apoptotic cell and the phagocyte. The bridging property of Protein S enhances the phagocytosis ... occurring. Pathology Mutations in the PROS1 gene can lead to Protein S deficiency ... of, and molecular defects underlying, inherited protein S deficiency in the general population ... Prior P, Hurtado B, Sala N title Molecular basis of protein S deficiency journal Thromb. Haemost ... Protein S has been shown to Protein protein interaction interact with Factor V . ref name pmid10593904 ... J, Tans G, Griffin J H year 1999 month Dec. title C terminal residues 621 635 of protein S are essential ... coauthors Mesters R M, Tans G, Rosing J, Griffin J H year 1993 month Feb. title Binding of protein ...   more details



  1. Data

    dablink For data in a computer science context, see Data computing . For other senses of the word, see Data disambiguation . See also datum , a disambiguation page. pp move indef Editors please keep the count mass discussion and etymology in the body, not the intro. The term data refers to qualitative or quantitative attributes of a variable mathematics variable or set of variables. Data plural of datum are typically the results of measurements and can be the basis of graph data structure graph s, image s, or observations of a set of variables. Data are often viewed as the lowest level of abstraction from which information and then knowledge are derived. Raw data , i.e. unprocessed data, refers ... that collect information to convert physical quantities into symbols. Etymology The word data pron ... . It is derived from ancient Persian word data . In discussions of problems in geometry , mathematics , engineering , and so on, the terms givens and data are used interchangeably. Also, data is a representation of a fact, figure, and idea. Such usage is the origin of data as a concept in computer science data are numbers, words, images, etc., accepted as they stand. Usage in English Weasel date ... data are measured. Any measurement or result is a datum , but data point is more common, ref cite ... . Both datums see usage in datum geodesy datum article and the originally Latin plural data are used as the plural of datum in English, but data is commonly treated as a mass noun and used with a verb ... the data from the experiment . This usage is inconsistent with the rules of Latin grammar and traditional English These are all the data from the experiment . Even when a very small quantity of data is referenced One number, for example the phrase piece of data is often used, as opposed to datum ... generic.xsl& publisher IEEE Computer Society ref allow usage of data as either a mass noun or plural ... data as a plural noun. For example, the Air Force Flight Test Center specifically states that the word ...   more details



  1. DATA

    otheruses Data disambiguation Debt, AIDS, Trade, Africa or DATA was a multinational Non governmental organization non government organization founded in January 2002 in London by U2 s Bono along with Robert Sargent Shriver III Bobby Shriver and activist s from the Jubilee 2000 Drop the Debt campaign. DATA was created for the purpose of obtaining social equality equality and justice for Africa through debt relief , adjusting trade rules which burden Africa, eliminating the AIDS in Africa African AIDS epidemic, strengthening democracy , more accountability by the wealthiest nations and African leaders and Transparency humanities transparency towards the people. In 2007, DATA and Bono were jointly awarded the National Constitution Center s 2007 Liberty Medal for their groundbreaking efforts to address the AIDS crisis and extreme poverty in Africa. Start up funds came from the Bill & Melinda Gates Foundation , financier George Soros , and technology entrepreneur Edward W. Scott . ref cite news url http www.time.com time printout 0,8816,1142270,00.html title The Constant Charmer author Josh Tyrangiel date 2005 12 19 work Time Magazine ref In 2007, DATA and the ONE Campaign decided to join forces, and in January 2008, they formally merged under the name ONE. ref cite news url http www.reuters.com article idUSN2953856520071029 title Bono s U.S. based anti poverty groups to merge author Lesley Wroughton date 2007 10 29 work Reuters ref DATA received support from the Christian rock Alternative rock bands Switchfoot and Third Day . References references External links http www.one.org ONE official site Category International nongovernmental organizations Category HIV AIDS in Africa Category Organizations founded by Bono int org stub de Debt, AIDS, Trade in Africa it DATA vi DATA ...   more details



  1. Dodecameric protein

    Dodecameric is a term pertaining to protein quaternary structure , and describes a protein complex with 12 protein subunits protein chain s . Dodecameric complexes can have a number of Protein subunit subunit topology topologies , but typically only a few of the theory theoretically possible subunit arrangement s are observed in protein structure s. A dodecamer is a protein complex with 12 protein subunits. A common Protein subunit subunit arrangement involves a tetrahedral distribution of subunit protein trimer trimer s or 3 4 Point groups in three dimensions point symmetry . Another observed arrangement of Protein subunit subunits puts two rings of six subunits side by side along the six fold axis or 2 6 point symmetry . Dodecameric proteins include Complete gap junction channel, composed of two hexamers. glutamine synthetase PDB code http www.pdbe.org 2gls 2gls Dodecameric ferritin PDB code http www.pdbe.org 1qgh 1qgh A 42 Amyloid beta 42 References Protein Data Bank The Protein Data Bank PDB http www.ebi.ac.uk msd srv prot int cgi bin piserver The Protein Quaternary Structure Server PQS part of the http www.ebi.ac.uk pdbe PDBe . Category Protein structure biochem stub ...   more details



  1. Protein?protein interaction prediction

    patterns This method ref Aytuna ref Ogmen builds a library of known protein protein interfaces from the Protein Data Bank PDB , where the interfaces are defined as pairs of polypeptide fragments ... between pairs of targets, providing that they have a known structure i.e. present in the Protein Data Bank PDB . Bayesian network modelling Bayesian method s ref Jansen integrate data from a wide variety ... networks approach for predicting protein protein interactions from genomic data. Science , 302 5644 ... the data from PPIPs or experimentally verified interaction maps to infer protein interaction for evolutionarily ...Expert subject Biology date November 2008 Protein protein interaction prediction is a field combining ... pairs or groups of proteins. Understanding protein protein interaction s is important for the investigation of intracellular signaling pathways, modelling of protein complex structures and for gaining ... screening two hybrid systems, protein fragment complementation assays PCA , affinity purification mass spectrometry , protein microarray s, fluorescence resonance energy transfer FRET and Microscale ... proteins have fused orthologues in other organisms. In addition, a number of bound protein ... profiling ref Pellegrini finds pairs of protein families with similar patterns of presence ... process, but does not necessarily imply physical interaction. Prediction of co evolved protein ... distance matrices are calculated for each protein in the hypothesized interacting pair. If the matrices ... to assess the likelihood that a particular potential protein interaction is a true positive ... might interact. 3D template based protein complex modelling This method ref Aloy ref Chen ref Fukuhara ref Kittichotirat makes use of known protein complex structures to predict as well as structurally model interactions between query protein sequences. The prediction process generally starts by employing a sequence based method e.g Interolog to search for protein complex structures that are homologous ...   more details



  1. S-Bank

    Dablink S Bank redirects here. For the Iranian investment bank, see S Bank Iran . Infobox Company company name S Bank Ltd company logo Image S pankkilogo.png 200px company type Private foundation 2006 location Helsinki , Finland industry Financial services products Deposit banking homepage http www.s pankki.fi S Bank Ltd S pankki Oy is the bank of the S Group Finnish S ryhm , a Finnish retailing cooperative organisation. S Bank is the first so called supermarket bank in Finland. Changes in legislation about personal accounts at co operatives made them uncompetitive, such that founding an entirely new bank was actually easier than keeping the personal accounts as co operative funds. The co operative did, and the bank continued to, offer a relatively high interest to deposited funds. It was 2.5 in February 2008, although this was cut to 0.2 due to the global recession since 2008. The existing network of supermarket service desks is used to service customers. However, Internet based electronic banking is recommended and provided at no cost to the customer. Visa credit and debit cards are available. Members of Euro Banking Association Category Banks of Finland Category Supermarket banks Category Banks established in 2006 Category Cooperative banking Euro bank stub fi S Pankki ...   more details



  1. T Bank

    Infobox Company company name TBank br small formerly Aspis Bank small company logo File T Bank logo.JPG 250px company type Bank company slogan Hugs our life foundation 1992 location Athens , Greece key people num employees industry products owner TT Hellenic Postbank lang el revenue 2.8 billion 2009 homepage http www.aspisbank.gr www.aspisbank.gr File Aspis Bank logo.jpg right thumb The logo of the bank before the rebranding TBank formerly Aspis Bank lang el is a commercial bank in Greece . Its headquarters are in Athens , and has 72 branches across Greece as of September 2008. The bank is traded on the Athens Stock Exchange . Aspis Bank was rebranded as TBank on 7 May 2010, following its acquisition by TT Hellenic Postbank lang el ref http www.capital.gr Articles.asp?id 964001 Greek ref References Reflist Category Banks of Greece Category Companies listed on the Athens Stock Exchange Category Companies of Greece greece stub Euro bank stub fr Liste d entreprises grecques ro Companii grecesti ...   more details



  1. Protein crystallization

    , Bourne P title The Protein Data Bank journal Nucleic Acids Research volume 28 issue 1 pages 235 242 year 2000 pmid 10592235 pmc 102472 doi 10.1093 nar 28.1.235 ref . Since then, the pace at which protein ...&pg PP1 v onepage&q&f false isbn 9780125870733 unused data loca tion San Diego ref . The importance of protein ... protein structure was slow due to the difficulty inherent in crystallizing proteins. When the Protein Data Bank http www.pdb.org was founded in 1971, it contained only seven structures ref name Berman .... File Protein crystals grown in space.jpg thumb Crystals of proteins grown on the United States ... to form crystals when placed in the appropriate conditions. In order to crystallize a protein, the purified protein undergoes slow precipitation from an aqueous solution. As a result, individual protein ... protein is used to determine the protein s three dimensional structure via X ray diffraction. In 1934, John Desmond Bernal and his student Dorothy Hodgkin discovered that protein crystals surrounded ... the first to discern the diffraction pattern of a wet, globular protein. Prior to Bernal and Hodgkin, protein crystallography had only been performed in dry conditions with inconsistent and unreliable results ref name Tulinksi cite journal author Tulinksi, A title The Protein Structure Project, 1950 1959 First Concerted Effort Of a Protein Structure Determination In the U.S. journal The Rigaku ... protein crystal used successfully in X ray diffraction. PDB ID 3PSG The goal of crystallization is to produce ... the protein s tertiary structure . Protein crystallization is inherently difficult because of the fragile nature of protein crystals. Proteins have irregularly shaped surfaces, which results in the formation of large channels within any protein crystal. Therefore, the noncovalent bonds that hold ... . In addition to overcoming the inherent fragility of protein crystals, a number of environmental ... unique to each protein must be obtained for a successful crystallization. Therefore, attempting to crystallize ...   more details



  1. STRIDE (protein)

    Orphan date February 2009 In protein structure , STRIDE Str uctural ide ntification is an algorithm for the assignment of protein secondary structure elements given the atomic coordinates of the protein, as defined by X ray crystallography , protein NMR , or another protein structure determination method. In addition to the hydrogen bond criteria used by the more common DSSP protein DSSP algorithm, the STRIDE assignment criteria also include dihedral angle potentials. As such, its criteria for defining individual secondary structures are more complex than those of DSSP. The STRIDE potential function energy function contains a hydrogen bond term containing a Lennard Jones potential Lennard Jones like 8 6 distance dependent potential and two angular dependence factors reflecting the planar ity of the optimized hydrogen bond geometry. The criteria for individual secondary structural elements, which are divided into the same groups as those reported by DSSP, also contain statistical probability factors derived from empirical examinations of solved structures with visually assigned secondary structure elements extracted from the Protein Data Bank . Although DSSP is the older method and continues to be the most commonly used, the original STRIDE definition reported it to give a more satisfactory structural assignment in at least 70 of cases. In particular, STRIDE was observed to correct for the propensity of DSSP to assign shorter secondary structures than would be assigned by an expert crystallographer, usually due to the minor local variations in structure that are most common near ... based protein secondary structure assignment. Proteins 23 4 566 79. DOI 10.1002 prot.340230412 ... name Martin Martin J, Letellier G, Marin A, Taly JF, de Brevern AG, Gibrat JF. 2005 . Protein secondary ... S. 2002 . Occurrence, conformational features and amino acid propensities for the pi helix. Protein ... Category Protein structure ...   more details



  1. Protein farnesyltransferase

    enzyme Name protein farnesyltransferase EC number 2.5.1.58 CAS number IUBMB EC number 2 5 1 58 GO code 0004660 image width caption In enzymology , a protein farnesyltransferase EC number 2.5.1.58 is an enzyme that catalysis catalyzes the chemical reaction farnesyl diphosphate protein cysteine math rightleftharpoons math S farnesyl protein diphosphate Thus, the two substrate biochemistry substrates of this enzyme are farnesyl diphosphate and protein cysteine , whereas its two product chemistry products are S farnesyl protein and diphosphate . This enzyme belongs to the family of transferase s, specifically those transferring aryl or alkyl groups other than methyl groups. The systematic name of this enzyme class is farnesyl diphosphate protein cysteine farnesyltransferase . This enzyme is also called FTase . Structural studies As of late 2007, 15 tertiary structure structures have been solved for this class of enzymes, with Protein Data Bank PDB accession codes PDB link 1S63 , PDB link 1S64 , PDB link 1SA4 , PDB link 1SA5 , PDB link 1TN6 , PDB link 1TN7 , PDB link 1TN8 , PDB link 1X81 , PDB link 2BED , PDB link 2F0Y , PDB link 2H6F , PDB link 2H6G , PDB link 2H6H , PDB link 2H6I , and PDB link 2IEJ . References reflist 1 cite journal author Furfine ES, Leban JJ, Landavazo A, Moomaw JF, Casey PJ date 1995 title Protein farnesyltransferase kinetics of farnesyl pyrophosphate binding and product release journal Biochemistry. volume 34 pages 6857&ndash 62 pmid 7756316 doi 10.1021 bi00020a032 issue 20 cite journal author Casey PJ, Seabra MC date 1996 title Protein prenyltransferases journal J. Biol. Chem. volume 271 pages 5289&ndash 92 pmid 8621375 doi 10.1074 jbc.271.10.5289 issue 10 cite journal author Long SB, Casey PJ, Beese LS date 1998 title Cocrystal structure of protein ... KA, Isaacs RJ, Andres DA, Spielmann HP date 2001 title Protein farnesyltransferase isoprenoid substrate ... Long SB, Casey PJ, Beese LS date 2002 title Reaction path of protein farnesyltransferase at atomic ...   more details



  1. Protein?protein interaction screening

    protein interaction data for yeast organisms check my plural the singular looked very wrong . cross link Chemical crosslinking is often used to fix protein interactions in place before trying to isolate ...The screening of protein protein interactions refers to the identification of protein interactions with high throughput screening methods such as computer and or robot assisted plate reading, flow cytometry ... for new therapeutic approaches. Methods to screen protein protein interactions Though there are many methods to detect protein protein interactions, the majority of these methods such as Co immunoprecipitation ... approaches. Ex vivo or in vivo methods Methods that screen protein protein interactions ... of protein protein interactions and their modulators. ref cite journal author Lu JP, Beatty LK, Pinthus ... screening and verification of protein interactions in living cells journal Nature Precedings ... of a protein without bias. However, the method has a notoriously high false positive rate, which makes ... as by co immunoprecipitation . However, the TAP tag method requires two successive steps of protein purification, and thus can not readily detect transient protein protein interactions. Recent genome ... H year 2006 volume 40 issue 4 pages 423, 425, 427 title Protein microarrays journal Biotechniques pmid 16629388 ref See also Protein protein interaction BiFC References Reflist External links External links date August 2010 Protein protein interaction databases http hprd.org HPRD Human Protein Reference Database , a manually curated database of human protein information with visualization tools http ... interaction data from the literature http dip.doe mbi.ucla.edu DIP Database of Interacting Proteins ... verified protein interactions mined from the literature by curators http mips.gsf.de proj ppi MIPS Mammalian Protein Protein Interaction Database , the MIPS mammalian protein protein interaction database http www.thebiogrid.org BioGRID genomics footer Biology footer DEFAULTSORT Protein Protein ...   more details




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