BioModelsapplication/xmlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1507180048?filename=MODEL1507180048.pdfhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1507180048?filename=MODEL1507180048-biopax3.owlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1507180048?filename=MODEL1507180048-biopax2.owlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1507180048?filename=MODEL1507180048_url.xmlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1507180048?filename=MODEL1507180048_urn.xmlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1507180048?filename=MODEL1507180048.xpphttps://www.ebi.ac.uk/biomodels/model/download/MODEL1507180048?filename=MODEL1507180048.scihttps://www.ebi.ac.uk/biomodels/model/download/MODEL1507180048?filename=MODEL1507180048.pnghttps://www.ebi.ac.uk/biomodels/model/download/MODEL1507180048?filename=MODEL1507180048.vcmlhttps://www.ebi.ac.uk/biomodels/model/download/MODEL1507180048?filename=MODEL1507180048.mprimaryOK200Nicolas Le NovèreNon-curatedconstraint-based modelL3V1https://www.ebi.ac.uk/biomodels/MODEL150718004819762644falseBioModelsSBMLModelsZhang2009 Genome scale metabolic network of Thermotoga maritima2009MODEL1507180048Non KineticYing Zhang, Ines Thiele, Dana Weekes, Zhanwen Li, Lukasz Jaroszewski, Krzysztof Ginalski, Ashley M Deacon, John Wooley, Scott A Lesley, Ian A Wilson, Bernhard Palsson, Andrei Osterman, Adam GodzikYing Zhang19762644, Metabolic pathways have traditionally been described in terms of biochemical reactions and metabolites. With the use of structural genomics and systems biology, we generated a three-dimensional reconstruction of the central metabolic network of the bacterium Thermotoga maritima. The network encompassed 478 proteins, of which 120 were determined by experiment and 358 were modeled. Structural analysis revealed that proteins forming the network are dominated by a small number (only 182) of basic shapes (folds) performing diverse but mostly related functions. Most of these folds are already present in the essential core (approximately 30%) of the network, and its expansion by nonessential proteins is achieved with relatively few additional folds. Thus, integration of structural data with networks analysis generates insight into the function, mechanism, and evolution of biological networks.. 5947, 325. Joint Center for Molecular Modeling (JCMM), Burnham Institute for Medical Research, La Jolla, CA 92037, USA.n.lenovere@gmail.comThe Babraham InstituteMetabolic pathways have traditionally been described in terms of biochemical reactions and metabolites. With the use of structural genomics and systems biology, we generated a three-dimensional reconstruction of the central metabolic network of the bacterium Thermotoga maritima. The network encompassed 478 proteins, of which 120 were determined by experiment and 358 were modeled. Structural analysis revealed that proteins forming the network are dominated by a small number (only 182) of basic shapes (folds) performing diverse but mostly related functions. Most of these folds are already present in the essential core (approximately 30%) of the network, and its expansion by nonessential proteins is achieved with relatively few additional folds. Thus, integration of structural data with networks analysis generates insight into the function, mechanism, and evolution of biological networks.Three-dimensional structural view of the central metabolic network of Thermotoga maritima.Zhang Ying Y, Thiele Ines I, Weekes Dana D, Li Zhanwen Z, Jaroszewski Lukasz L, Ginalski Krzysztof K, Deacon Ashley M AM, Wooley John J, Lesley Scott A SA, Wilson Ian A IA, Palsson Bernhard B, Osterman Andrei A, Godzik Adam Ascale tissue, whole genome, scales, peltate hair., scale, Genomes, plant peltate hairsmall, extent, scale tissue, data, Sectors, Genomics, Public Sectors, PLXN5, determination, completeness, Comparative, peltate hair, Proteins, number, Nl1, Gene, PLEXIN-B1, Mell1, Copyrights, function, Functional Genomics, presence, SeP, sep5, count in organism, Experiment, CEH, Structural, reduced, MMEL2, Public, Public Domain, Systems, Protein, chemical analysis, Functional, Gene Products, Domains, core, NEPII, NL1, NL2, tiny, scales, SEH, Public Enterprise, Enterprises, Domain, Data Base, SEP, Sep, CG2916, scale, Genomes, Biology, underdeveloped, plant peltate hair, Comparative Genomics, Public Domains, DmelCG2916, hypoplasia, Sciences, proteins, whole genome, Public Enterprises, sEP, Protein Gene Products, Gene Proteins, Abstract, Sector, cardinality, SELP, Structural Genomics, Eph2, Public., assay, Enterprise, NEP2small, Metabolic Networks, Networks, data, Pathway, Genomics, function., Metabolic, Biology, determination, underdeveloped, Comparative, Comparative Genomics, Proteins, number, hypoplasia, secondary metabolites, metabolite, Pathways, Gene, proteins, Network, Metabolic Network, Functional Genomics, presence, Protein Gene Products, Gene Proteins, count in organism, primary metabolites, Experiment, Structural, reduced, metabolites, Systems, Protein, chemical analysis, cardinality, Functional, Gene Products, core, Metabolic Pathway, Structural Genomics, assay, tiny, Metabolic PathwaysfalseZhang2009 - Genome-scale metabolic network of Thermotoga maritima Zhang2009 - Genome-scale metabolic network of Thermotoga maritima This model is described in the article: Three-dimensional structural view of the central metabolic network of Thermotoga maritima. Zhang Y, Thiele I, Weekes D, Li Z, Jaroszewski L, Ginalski K, Deacon AM, Wooley J, Lesley SA, Wilson IA, Palsson B, Osterman A, Godzik A. Science 2009 Sep; 325(5947): 1544-1549 Abstract: Metabolic pathways have traditionally been described in terms of biochemical reactions and metabolites. With the use of structural genomics and systems biology, we generated a three-dimensional reconstruction of the central metabolic network of the bacterium Thermotoga maritima. The network encompassed 478 proteins, of which 120 were determined by experiment and 358 were modeled. Structural analysis revealed that proteins forming the network are dominated by a small number (only 182) of basic shapes (folds) performing diverse but mostly related functions. Most of these folds are already present in the essential core (approximately 30%) of the network, and its expansion by nonessential proteins is achieved with relatively few additional folds. Thus, integration of structural data with networks analysis generates insight into the function, mechanism, and evolution of biological networks. This model is hosted on BioModels Database and identified by: MODEL1507180048. To cite BioModels Database, please use: BioModels Database: An enhanced, curated and annotated resource for published quantitative kinetic models. To the extent possible under law, all copyright and related or neighbouring rights to this encoded model have been dedicated to the public domain worldwide. Please refer to CC0 Public Domain Dedication for more information. 2015-07-282015-07-302015-07-18MODEL150718004819762644MODEL1507180048