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Encyclopedia results for Protein Data Bank

Protein Data Bank





Encyclopedia results for Protein Data Bank

  1. Worldwide Protein Data Bank

    The Worldwide Protein Data Bank , wwPDB, is an organization that maintains the archive of macromolecules macromolecular structure . Its mission is to maintain a single Protein Data Bank Archive of macromolecular structural data that is freely and publicly available to the global community. ref Worldwide Protein Data Bank. URL http www.wwpdb.org http www.wwpdb.org . Accessed on April 22, 2009. ref ref ... Protein Data Bank journal Nat. Struct. Biol. volume 10 issue 12 pages 980 year 2003 month December ... date title The worldwide Protein Data Bank wwPDB ensuring a single, uniform archive of PDB data ... 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 Category Biological ... Berman last H. authorlink coauthors et al. year 2008 month January date title Remediation of the protein data bank archive journal Nucleic Acids Res. volume 36 issue Database issue pages D426 D433 doi ... 10&hits 10&RESULTFORMAT &fulltext Protein Data Bank&searchid 1&FIRSTINDEX 0&resourcetype HWCIT format accessdate 1 3 2008 quote pmid 18073189 pmc 2238854 ref References references See also Protein Data Bank External links The parent organization http www.wwpdb.org wwPDB The four member organizations ... pmid 17142228 pmc 1669775 ref Research Collaboratory for Structural Bioinformatics Protein Database RCSB PDB Protein Data Bank in Europe PDBe Protein Data Bank Japan PDBj Biological Magnetic Resonance Data Bank BMRB The wwPDB was founded in 2003 by RCSB PDB USA , PDBe Europe and PDBj Japan . In 2006 BMRB USA joined the wwPDB. Each member s site can accept structural data and process the data. The processed data is sent to the archive keeper . The RCSB PDB presently acts as the archive keeper . This ensures that there is only one version of the data which is identical for all users. The modified ... files available through their websites to the public. Data is accessed from the wwPDB website ...   more details



  1. Protein Data Bank

    infobox biodatabase title The Protein Data Bank. logo File Database.png description Protein structure ... scope organism center laboratory author pmid released standard format Protein Data Bank file ... 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 ... www.rcsb.org RCSB . The PDB is overseen by an organization called the Worldwide Protein Data Bank ... title The Protein Data Bank a historical perspective pmid 18156675 journal Acta Crystallographica ... author Meyer EF year 1997 title The first years of the Protein Data Bank journal Protein Science ... The Protein Data Bank journal Nucleic Acids Res. volume 28 issue 1 pages 235 242 doi 10.1093 nar 28.1.235 ... RCSB Protein Data Bank url http www.rcsb.org pdb static.do?p general information news publications ... of Worldwide Protein Data Bank wwPDB can act as deposition, data processing and distribution centers ... was called the Protein Data Bank file format PDB file format . This original format was restricted ... 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 www.pdbj.org ... bg Protein Data Bank 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 simple Protein Data Bank sr Proteinska banka podataka fi Protein Data Bank sv Protein Data Bank uk zh ... to initiate the PDB 1 a small but growing collection of sets of protein structure data determined ... Protein structure Protein structure databases PDBsum &mdash extracts data from other databases ...   more details



  1. Protein circular dichroism data bank

    Orphan date April 2011 infobox biodatabase title PCDDB logo File Database.png description circular dichroism spectral and metadata. scope organism center Birkbeck College , University of London laboratory Department of Crystallography, Institute of Structural and Molecular Biology author Lee Whitmore pmid Whitmore & al. 2011 ref name pmid21071417 released 2010 standard format url http pcddb.cryst.bbk.ac.uk download webservice sql sparql webapp standalone license versioning frequency curation bookmark version The Protein Circular Dichroism Data Bank PCDDB is a database of circular dichroism and synchrotron radiation . ref name pmid21071417 cite journal quotes yes last Whitmore first Lee authorlink coauthors Woollett Benjamin, Miles Andrew John, Klose D P, Janes Robert W, Wallace B A year 2011 month Jan title PCDDB the Protein Circular Dichroism Data Bank, a repository for circular dichroism spectral and metadata journal Nucleic Acids Res. volume 39 issue Database issue pages D480 6 publisher location England issn pmid 21071417 doi 10.1093 nar gkq1026 bibcode oclc id url pmc 3013654 language eng format accessdate laysummary laysource laydate quote ref References references See also circular dichroism synchrotron radiation External links http pcddb.cryst.bbk.ac.uk. Biodatabase stub Category Biological databases Category Polarization Category Protein structure Category Electromagnetic radiation ...   more details



  1. Protein Data Bank (file format)

    www.rcsb.org pdb The RCSB Protein Data Bank http www.pdbe.org Protein Data Bank in Europe MMDB The Molecular ... of the atoms that are part of the protein. For example, the first ATOM line above describes ... are not part of the protein molecule. Through the years the file format has undergone many changes ... Category Chemical file formats Category Biological databases 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 . In computers the databank is same as that of we use in telecommunication i.e. it is the repository of data.The data in the databank can be any data like credit card transaction of a store or it can be any data base of a company where 1000 of queries are being processed on daily bases. 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 Practitioner Data Bank

    reason Need body text & context. date March 2012 Background The Data Bank comprises both the National Practitioner Data Bank NPDB and the Healthcare Integrity and Protection Data Bank HIPDB . Each Data ... care fraud and abuse in the U.S. The Data Bank is primarily an alert or flagging system for registered ... the Data Bank should be used in conjunction with, not in replacement of, information from other sources. ref name The Data Bank Website About Us http www.npdb hipdb.hrsa.gov topNavigation aboutUs.jsp The Data Bank Website About Us ref Overview The National Practitioner Data Bank and the Healthcare Integrity and Protection Data Bank were created under different laws and have separate governing regulations. In addition, there are other important Federal laws that play a vital role in Data Bank operations. National Practitioner Data Bank NPDB http www.npdb hipdb.hrsa.gov resources titleIv.jsp The Data ... 1921.jsp The Data Bank Web site Section 1921 of the Social Security Act http www.npdb hipdb.hrsa.gov resources titleIv.jsp The Data Bank Web site About Us Health Care Integrity and Protection Data Bank HIPDB http www.npdb hipdb.hrsa.gov topNavigation aboutUs.jsp The Data Bank Web site Section 1128E of the Social Security Act http bhpr.hrsa.gov dpdb Practitioner Data Bank Website Eligibility ... in each of the Data Banks. ref name The Data Bank Web site The Data Bank at a Glance http www.npdb hipdb.hrsa.gov topNavigation aboutUs.jsp The Data Bank Web site The Data Bank at a Glance ref Table ... plans Confidentiality http www.npdb hipdb.hrsa.gov topNavigation aboutUs.jsp The Data Bank Web site Confidentiality of Data Bank Information General Public https www.ncsbn.org 418.htm National Council ... hcorg aboutQuerying.jsp The Data Bank Web site Querying Practitioner, Provider or Supplier http www.npdb hipdb.hrsa.gov pract whenToSearchForReports.jsp The Data Bank Web site When to Search for Your Own Reports Reporting http www.npdb hipdb.hrsa.gov hcorg aboutReporting.jsp The Data Bank Website ...   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 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 Health in the United States ...   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. DNA Data Bank of Japan

    Deleted image removed Image DDBJ.jpg right thumb 300px infobox biodatabase title DNA Data Bank of Japan logo File Database.png description Japanese DNA data bank scope organism all center International Nucleotide Sequence Database Collaboration br National Institute of Genetics laboratory Center for Information Biology and DNA Data Bank of Japan author pmid PMID 11752245 released 1986 standard format url http www.ddbj.nig.ac.jp download webservice sql sparql webapp standalone license versioning frequency curation bookmark version The DNA Data Bank of Japan DDBJ is a biological database that collects DNA sequences. ref name pmid11752245 cite journal author Tateno Y, Imanishi T, Miyazaki S, Fukami Kobayashi K, Saitou N, Sugawara H et al. title DNA Data Bank of Japan DDBJ for genome scale research in life science. journal Nucleic Acids Res year 2002 volume 30 issue 1 pages 27 30 pmid 11752245 url http www.ncbi.nlm.nih.gov entrez eutils elink.fcgi?dbfrom pubmed&tool clinical.uthscsa.edu cite&retmode ref&cmd prlinks&id 11752245 pmc 99140 doi 10.1093 nar 30.1.27 ref ref name pmid21062814 cite journal author Kaminuma E, Kosuge T, Kodama Y, et al. title DDBJ progress report journal Nucleic Acids Res. volume 39 issue Database issue pages D22 7 year 2011 month January pmid 21062814 pmc 3013661 doi 10.1093 nar gkq1041 url ref It is located at the National Institute of Genetics NIG in the Shizuoka prefecture of Japan. It is also a member of the International Nucleotide Sequence Database Collaboration or INSDC . It exchanges its data with European Molecular Biology Laboratory at the European ... site http biodatabase.org index.php DDBJ DNA Data Bank of Japan DDBJ entry in MetaBase . Category ... on a daily basis. Thus these three databanks contain the same data at any given time. DDBJ began data bank activities in 1986 at NIG and remains the only nucleotide sequence data bank in Asia. Although DDBJ mainly receives its data from Japanese researchers, it can accept data from contributors from ...   more details



  1. EM Data Bank

    for molecular microscopy http emdatabank.org EM Data Bank http emdatabank.org search.html US and UK ...infobox biodatabase title EMDataBank.org logo File Database.png description Unified Data Resource for CryoEM . center European Bioinformatics Institute UK site AND Rutgers University USA site laboratory PDBe & RCSB PDB pmid Lawson & al. 2011 ref name pmid20935055 cite journal quotes yes last Lawson first Catherine L authorlink coauthors Baker Matthew L, Best Christoph, Bi Chunxiao, Dougherty Matthew, Feng Powei, van Ginkel Glen, Devkota Batsal, Lagerstedt Ingvar, Ludtke Steven J, Newman Richard H, Oldfield Tom J, Rees Ian, Sahni Gaurav, Sala Raul, Velankar Sameer, Warren Joe, Westbrook John D, Henrick Kim, Kleywegt Gerard J, Berman Helen M, Chiu Wah year 2011 month Jan title EMDataBank.org unified data resource for CryoEM journal Nucleic Acids Res. volume 39 issue Database issue pages D456 64 publisher location England issn pmid 20935055 doi 10.1093 nar gkq880 bibcode oclc id url pmc 3013769 language eng format accessdate laysummary laysource laydate quote ref released 2002 standard format url http emdatabank.org download webservice sql sparql webapp standalone license versioning frequency curation bookmark version 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 European Bioinformatics Institute European Bioinformatics Institute EBI , where the European site of the 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 ... M. Tagari, et al. 2006 . E MSD improving data deposition and structure quality . Nucleic Acids Res, 34 Database issue pp. 287 290. PMID 16381867 C. Lawson, et al. EMDataBank.org unified data resource ...   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. Current Chairs of the SRP are Dr. Finis Cavender, Toxicology Group, and Dr. Roland Everett Langford, Environmental Fate Group. 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 TV Public access television 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 ....html ref In 1976 Horsfield and Blumenthal officially founded the Video Data Bank, taking over a small ... 2007. In 2007 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 ... eds. year 2006 title Feedback The Video Data Bank Catalog of Video Art and Artist Interviews ..., 1996. External links 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 ...   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

    are usually deposited in the Protein Data Bank PDB , a freely available resource from which structural ... Data Bank has over 55,000 atomic resolution structures of proteins. ref name urlRCSB Protein Data Bank In more recent times, cryo electron microscopy of large macromolecular assemblies ref ...About a class of molecules protein as a nutrient Protein nutrient other uses pp semi indef File Myoglobin.png 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 ... folded into a globular protein globular or fibrous protein fibrous form, facilitating a biological ... . The peptide sequence sequence of amino acids in a protein is defined by the DNA sequence sequence ... archaea pyrrolysine . Shortly after or even during synthesis, the residues in a protein are often ... to form stable protein complex es. Like other biological macromolecules such as polysaccharide ... acid s from food. Through the process of digestion , animals break down ingested protein into free amino acids that are then used in metabolism. Proteins may be protein purification purified from ... made possible a number of methods to facilitate purification. Methods commonly used to study protein ... chains in a protein that ultimately determines its three dimensional structure and its chemical reactivity ... linked in the protein chain, an individual amino acid is called a residue, and the linked series of carbon, nitrogen, and oxygen atoms are known as the main chain or protein backbone. ref Murray ... structures of the peptide bond that links individual amino acids to form a protein polymer The peptide ... angle s in the peptide bond determine the local shape assumed by the protein backbone. ref Murray et al ., p. 31. ref The end of the protein with a free carboxyl group is known as the C terminus .... The words protein , polypeptide, and peptide are a little ambiguous and can overlap in meaning ...   more details



  1. Protein A

    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



  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 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 Protein protein interaction interact with Factor ... 621 635 of protein S are essential for binding to factor Va journal J. Biol. Chem. volume 274 issue ... Feb. title Binding of protein S to factor Va associated with inhibition of prothrombinase that is independent ...   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.pdbe.org pisa Protein Interfaces, Surfaces and Assemblies Server PISA part of the http www.pdbe.org PDBe . Category Protein structure biochem stub ...   more details



  1. Data

    two other uses data in computer science Data computing pp move indef Editors please keep the count mass discussion and etymology in the body, not the intro. Data IPAc en icon d e t respell DAY t , IPAc en d t respell DA t , or IPAc en d t respell DAH t are values of Qualitative data qualitative or Quantitative data quantitative variable and attribute research variable s, belonging to a set of items. Data in computing or data processing are often represented by a combination of items organized in rows and multivariate analysis multiple variables organized in columns. Data are typically the results of measurements and can be data visualisation visualised using graph data structure graph s or image s. Data as an abstract concept can be viewed as the lowest level of abstraction from which information and then knowledge are derived. Raw data , i.e., unprocessed data, refers to a collection of number s, character computing characters and is a relative term data processing commonly occurs by stages, and the processed data from one stage may be considered the raw data of the next. Field work Field data refers to raw data collected in an uncontrolled in situ environment. Experimental data refers to data generated within the context of a scientific investigation by observation and recording. The word data is the plural of datum , Grammatical gender neuter past participle ... , engineering , and so on, the terms givens and data are used interchangeably. Such usage is the origin of data as a concept in computer science or data processing data are numbers, words, images ... datum from which distances to all other data are measured. Any measurement or result is a datum , but data point is more usual, ref cite web author Matt Dye year 2001 title Writing Reports url http ... and the originally Latin plural data are used as the plural of datum in English, but data is commonly ... in day to day usage. For example, This is all the data from the experiment . This usage is inconsistent ...   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 purposes 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 furthering 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 sv DATA f rening vi DATA ...   more details



  1. Protein?protein interaction prediction

    ref Ogmen builds a library of known protein protein interfaces from the Protein Data Bank PDB , where ... 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 of sources, including both experimental ... protein interactions from genomic data. Science , 302 5644 449 53. note Aloy Aloy P., and R. B ... protein complexes by a consensus neural network method Test against NMR data. Proteins 61 21 ...., Juan, David.& Valencia, Alfonso. 2004 . Accessible Protein Interaction Data for Network Modeling ...Protein protein interaction prediction is a field combining bioinformatics and structural biology in an attempt ... protein protein interaction s is important for the investigation of intracellular signaling pathways, modelling of protein complex structures and for gaining insights into various biochemical ... of experimental techniques, including yeast two hybrid screening two hybrid systems, protein fragment complementation assays PCA , affinity purification mass spectrometry , protein microarray s, fluorescence ... in other organisms. In addition, a number of bound protein complexes have been structurally solved ... pairs of protein families with similar patterns of presence or absence across large numbers of species ... imply physical interaction. Prediction of co evolved protein pairs based on similar phylogenetic ... protein in the hypothesized interacting pair. If the matrices are sufficiently similar as measured ... potential protein interaction is a true positive result. These methods are useful because ... circumstantial evidence that a particular pair of proteins 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 ... to search for protein complex structures that are homologous to the query sequences. These known ...   more details



  1. Protein structure

    available in the Protein Data Bank have been determined by X ray crystallography . This method allows ...Refimprove date March 2009 In molecular biology protein structure describes the various levels of organization of protein molecules. Proteins are an important class of biological macromolecules present ... are nanoparticle s definition 1 100  nm . Each protein polymer also known as a polypeptide consists ... under 40 residues the term peptide is frequently used instead of protein. To be able to perform their biological ... field of structural biology , which employs techniques such as X ray crystallography , protein NMR NMR spectroscopy , and dual polarisation interferometry to determine the structure of proteins. Protein ... author Brocchieri L, Karlin S title Protein length in eukaryotic and prokaryotic proteomes date ... Acids Research pmc 1150220 ref Very large aggregates can be formed from protein subunit s for example, many thousand actin molecules assemble into a microfilament . A protein may undergo reversible structural changes in performing its biological function. The alternative structures of the same protein ... are called conformational change s. 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 ... together by Covalent bond covalent or peptide bond s, which are made during the process of protein biosynthesis ... where the amino group is not involved in a peptide bond. The primary structure of a protein is determined by the gene corresponding to the protein. A specific sequence of nucleotide s in DNA is Transcription .... The sequence of a protein is unique to that protein, and defines the structure and function of the protein. The sequence of a protein can be determined by methods such as Edman degradation or Mass spectrometry Protein identification tandem mass spectrometry . Often however, it is read directly ...   more details



  1. Protein farnesyltransferase

    Merge from Farnesyltransferase date January 2012 enzyme Name protein farnesyltransferase EC number 2.5.1.58 CAS number 131384 38 8 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 Further reading refbegin 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 ... author Long SB, Casey PJ, Beese LS date 1998 title Cocrystal structure of protein farnesyltransferase ..., Andres DA, Spielmann HP date 2001 title Protein farnesyltransferase isoprenoid substrate discrimination ... PJ, Beese LS date 2002 title Reaction path of protein farnesyltransferase at atomic resolution journal ...   more details



  1. Knotted protein

    Multiple issues wikify April 2012 orphan April 2012 The definition of the knotted protein Mathematically, a Knot mathematics knot is defined as a subset of a three dimensional points Homeomorphism homeomorphic to a circle. ref cite book last Cromwell first P. D. title Knots and Links year 2004 publisher Cambridge Cambridge University Press ref According to this definition, a knot only make senses for a closed loop. However, if we pick a point in space at infinity distance and connect to the N and C termini, respectively, through a virtual bond, the protein can be treated as a closed loop. File Pig1.png thumb A A protein is an open chain. B To create a closed loop, we pick a point at an infinity distance, and connect it to N and C termini and, thus, the whole topology structure become a closed loop. Introduction of the knotted protein Knotted proteins present one of the most challenging problems to both Computational biology computational and experimental biologists. Despite an ever increasing number of knotted proteins deposited in Protein Data Bank PDB , it is still not clear how a protein folds into a knotted conformation, or how a protein s knot is related to its function. Though a number of computational methods have been developed for detecting protein knots, there are still no completely automatic methods to detect protein knots without the necessary manual intervention due to the missing residues or chain breaks in the X ray structures or the nonstandard PDB formats. At present, there are 4 types of knot identified in proteins the 3 1 knot, the 4 1 knot, the 5 2 knot ... of convenience. The web server to extrapolate the knotted protein Recently, a number web servers ... protein knots. ref cite journal last Lai first Y. L. coauthors Yen, S. C., Yu, S. H., Hwang, J. K. title pKNOT the protein KNOT web server journal Nucleic Acids Research date 7 May 2007 volume ... pknot.life.nctu.edu.tw pKNOT Category Protein Category Computational biology pt Prote na atada ...   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




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