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STRENDA DB: enabling the validation and sharing of enzyme kinetics data
dc.contributor.authorSwainston, Neil
dc.contributor.authorBaici, Antonio
dc.contributor.authorBakker, Barbara M.
dc.contributor.authorCornish‐bowden, Athel
dc.contributor.authorFitzpatrick, Paul F.
dc.contributor.authorHalling, Peter
dc.contributor.authorLeyh, Thomas S.
dc.contributor.authorO’Donovan, Claire
dc.contributor.authorRaushel, Frank M.
dc.contributor.authorReschel, Udo
dc.contributor.authorRohwer, Johann M.
dc.contributor.authorSchnell, Santiago
dc.contributor.authorSchomburg, Dietmar
dc.contributor.authorTipton, Keith F.
dc.contributor.authorTsai, Ming‐daw
dc.contributor.authorWesterhoff, Hans V.
dc.contributor.authorWittig, Ulrike
dc.contributor.authorWohlgemuth, Roland
dc.contributor.authorKettner, Carsten
dc.date.accessioned2018-07-13T15:47:47Z
dc.date.available2019-08-01T19:53:24Zen
dc.date.issued2018-06
dc.identifier.citationSwainston, Neil; Baici, Antonio; Bakker, Barbara M.; Cornish‐bowden, Athel ; Fitzpatrick, Paul F.; Halling, Peter; Leyh, Thomas S.; O’Donovan, Claire; Raushel, Frank M.; Reschel, Udo; Rohwer, Johann M.; Schnell, Santiago; Schomburg, Dietmar; Tipton, Keith F.; Tsai, Ming‐daw ; Westerhoff, Hans V.; Wittig, Ulrike; Wohlgemuth, Roland; Kettner, Carsten (2018). "STRENDA DB: enabling the validation and sharing of enzyme kinetics data." The FEBS Journal 285(12): 2193-2204.
dc.identifier.issn1742-464X
dc.identifier.issn1742-4658
dc.identifier.urihttps://hdl.handle.net/2027.42/144658
dc.publisherWiley Periodicals, Inc.
dc.titleSTRENDA DB: enabling the validation and sharing of enzyme kinetics data
dc.typeArticleen_US
dc.rights.robotsIndexNoFollow
dc.subject.hlbsecondlevelMolecular, Cellular and Developmental Biology
dc.subject.hlbtoplevelHealth Sciences
dc.description.peerreviewedPeer Reviewed
dc.description.bitstreamurlhttps://deepblue.lib.umich.edu/bitstream/2027.42/144658/1/febs14427.pdf
dc.description.bitstreamurlhttps://deepblue.lib.umich.edu/bitstream/2027.42/144658/2/febs14427_am.pdf
dc.identifier.doi10.1111/febs.14427
dc.identifier.sourceThe FEBS Journal
dc.identifier.citedreferenceKim S, Thiessen PA, Bolton EE, Chen J, Fu G, Gindulyte A, Han L, He J, He S, Shoemaker BA et al. ( 2016 ) PubChem substance and compound databases. Nucleic Acids Res 44, D1202 â D1213.
dc.identifier.citedreferenceCarbonell P, Currin A, Jervis AJ, Rattray NJ, Swainston N, Yan C, Takano E & Breitling R ( 2016 ) Bioinformatics for the synthetic biology of natural products: integrating across the Designâ Buildâ Test cycle. Nat Prod Rep 33, 925 â 932.
dc.identifier.citedreferenceChang A, Schomburg I, Placzek S, Jeske L, Ulbrich M, Xiao M, Sensen CW & Schomburg D ( 2015 ) BRENDA in 2015: exciting developments in its 25th year of existence. Nucleic Acids Res 43, D439 â D446.
dc.identifier.citedreferenceWittig U, Kania R, Golebiewski M, Rey M, Shi L, Jong L, Algaa E, Weidemann A, Sauerâ Danzwith H, Mir S et al. ( 2012 ) SABIOâ RKâ database for biochemical reaction kinetics. Nucleic Acids Res 40, D790 â D796.
dc.identifier.citedreferenceWittig U, Rey M, Kania R, Bittkowski M, Shi L, Golebiewski M, Weidemann A, Müller W & Rojas I ( 2014 ) Challenges for an enzymatic reaction kinetics database. FEBS J 281, 572 â 582.
dc.identifier.citedreferenceWittig U, Kania R, Bittkowski M, Wetsch E, Shi L, Jong L, Golebiewski M, Rey M, Weidemann A, Rojas I et al. ( 2014 ) Data extraction for the reaction kinetics database SABIOâ RK. Perspect Sci 1, 33 â 40.
dc.identifier.citedreferenceLombard V, Golaconda RH, Drula E, Coutinho PM & Henrissat B ( 2014 ) The carbohydrateâ active enzymes database (CAZy) in 2013. Nucleic Acids Res 42, D490 â D495.
dc.identifier.citedreferenceApweiler R, Cornishâ Bowden A, Hofmeyr JH, Kettner C, Leyh TS, Schomburg D & Tipton K ( 2005 ) The importance of uniformity in reporting proteinâ function data. Trends Biochem Sci 30, 11 â 12.
dc.identifier.citedreferenceTipton KF, Armstrong RN, Bakker BM, Bairoch A, Cornishâ Bowden A, Halling PJ, Hofmeyr Jâ H, Leyh TS, Kettner C, Raushel FM et al. ( 2014 ) Standards for Reporting Enzyme Data: the STRENDA Consortium: what it aims to do and why it should be helpful. Perspect Sci 1, 131 â 137.
dc.identifier.citedreferenceVasilevsky NA, Brush MH, Paddock H, Ponting L, Tripathy SJ, LaRocca GM & Haendel MA ( 2013 ) On the reproducibility of science: unique identification of research resources in the biomedical literature. PeerJ 1, e148.
dc.identifier.citedreferenceLandis SC, Amara SG, Asadullah K, Austin CP, Blumenstein R, Bradley EW, Crystal RG, Darnell RB, Ferrante RJ, Fillit H et al. ( 2012 ) A call for transparent reporting to optimize the predictive value of preclinical research. Nature, 490, 187 â 191.
dc.identifier.citedreferenceGardossi L, Poulsen PB, Ballesteros A, Hult K, Svedas VK, Vasicâ Racki D, Carrea G, Magnusson A, Schmid A, Wohlgemuth R et al. ( 2010 ) Guidelines for reporting of biocatayltic reactions. Trends Biotechnol 28, 171 â 180.
dc.identifier.citedreferenceKolesnikov N, Hastings E, Keays M, Melnichuk O, Tang YA, Williams E, Dylag M, Kurbatova N, Brandizi M, Burdett T et al. ( 2015 ) ArrayExpress updateâ simplifying data submissions. Nucleic Acids Res 43, D1113 â D1116.
dc.identifier.citedreferenceVizcaíno JA, Csordas A, delâ Toro N, Dianes JA, Griss J, Lavidas I, Mayer G, Perezâ Riverol Y, Reisinger F, Ternent T et al. ( 2016 ) 2016 update of the PRIDE database and related tools. Nucleic Acids Res, 44, D447 â D456.
dc.identifier.citedreferenceHaug K, Salek RM, Conesa P, Hastings J, de Matos P, Rijnbeek M, Mahendraker T, Williams M, Neumann S, Roccaâ Serra P et al. ( 2013 ) MetaboLightsâ an openâ access generalâ purpose repository for metabolomics studies and associated metaâ data. Nucleic Acids Res 41, D781 â D786.
dc.identifier.citedreferenceRose WP, Prlic A, Bi C, Bluhm WF, Christie CH, Dutta S, Green RK, Goodsell DS, Westbrook JD, Woo J et al. ( 2015 ) The RCSB Protein Data Bank: views of structural biology for basic and applied research and education. Nucleic Acids Res 43, D345 â D356.
dc.identifier.citedreferenceBuchholz PC, Vogel C, Reusch W, Pohl M, Rother D, Spieà AC & Pleiss J ( 2016 ) BioCatNet: a database system for the integration of enzyme sequences and biocatalytic experiments. ChemBioChem 17, 2093 â 2098.
dc.identifier.citedreferenceUniProt Consortium ( 2015 ) UniProt: a hub for protein information. Nucleic Acids Res 43, D204 â D212.
dc.identifier.citedreferenceBerman HM, Kleywegt GJ, Nakamura H & Markley JL ( 2012 ) The Protein Data Bank at 40: reflecting on the past to prepare for the future. Structure 20, 391 â 396.
dc.identifier.citedreferenceMcDonald AG, Boyce S & Tipton KF ( 2009 ) ExplorEnz: the primary source of the IUBMB enzyme list. Nucleic Acids Res 37, D593 â D597.
dc.identifier.citedreferenceOgata H, Goto S, Sato K, Fujibuchi W, Bono H & Kanehisa M ( 1999 ) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 27, 29 â 34.
dc.identifier.citedreferenceHastings J, Owen G, Dekker A, Ennis M, Kale N, Muthukrishnan V, Turner S, Swainston N, Mendes P & Steinbeck C ( 2016 ) ChEBI in 2016: improved services and an expanding collection of metabolites. Nucleic Acids Res 44, D1214 â D1219.
dc.identifier.citedreferenceSwainston N, Hastings J, Dekker A, Muthukrishnan V, May J, Steinbeck C & Mendes P ( 2016 ) libChEBI: an API for accessing the ChEBI database. J Cheminform 8, 11.
dc.identifier.citedreferenceKrause F, Schulz M, Swainston N & Liebermeister W ( 2011 ) Sustainable model building the role of standards and biological semantics. Methods Enzymol 500, 371 â 395.
dc.identifier.citedreferenceLi P, Dada JO, Jameson D, Spasic I, Swainston N, Carroll K, Dunn W, Khan F, Malys N, Messiha HL et al. ( 2010 ) Systematic integration of experimental data and models in systems biology. BMC Bioinformatics 11, 582.
dc.identifier.citedreferenceVan Eunen K, Kiewiet JAL, Westerhoff HV & Bakker BM ( 2012 ) Testing biochemistry revisited: how in vivo metabolism can be understood from in vitro enzyme kinetics. PLoS Comput Biol 8, e1002483.
dc.identifier.citedreferenceSchnell S ( 2014 ) Validity of the Michaelisâ Menten equationâ steady state or reactant stationary assumption: that is the question. FEBS J 281, 464 â 472.
dc.identifier.citedreferenceSwainston N, Golebiewski M, Messiha HL, Malys N, Kania R, Kengne S, Krebs O, Mir S, Sauerâ Danzwith H, Smallbone K et al. ( 2010 ) Enzyme kinetics informatics: from instrument to browser. FEBS J 277, 3769 â 3779.
dc.owningcollnameInterdisciplinary and Peer-Reviewed


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