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MODEL1011300000 - Kim2010_VvuMBEL943_GSMR

 

The following model is part of the non-curated branch of BioModels Database. While the syntax of the model has been verified, its semantics remains unchecked. Any annotation present in the models is not a product of BioModels' annotators. We are doing our best to incorporate this model into the curated branch as soon as possible. In the meantime, we display only limited metadata here. For further information about the model, please download the SBML file.


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Reference Publication
Publication ID: 21245845
Kim HU, Kim SY, Jeong H, Kim TY, Kim JJ, Choy HE, Yi KY, Rhee JH, Lee SY.
Integrative genome-scale metabolic analysis of Vibrio vulnificus for drug targeting and discovery.
Mol. Syst. Biol. 2011 Jan; 7: 460
Metabolic and Biomolecular Engineering National Research Laboratory, Department of Chemical and Biomolecular Engineering (BK21 program), Korea Advanced Institute of Science and Technology (KAIST), Daejeon, Republic of Korea.  [more]
Model
Original Model: This submission version is...
Submitter: Hyun Uk Kim
Submission Date: 30 Nov 2010 15:46:29 UTC
Last Modification Date: 23 Jun 2011 14:13:11 UTC
Creation Date: 18 Jan 2011 23:34:34 UTC
Encoders:
bqbiol:isVersionOf Gene Ontology cellular metabolic process
bqbiol:hasTaxon Taxonomy Vibrio vulnificus
Notes

This is a model of the genome scale reconstruction of the Vibrio vulnificus metabolic network, VvuMBEL943, described in the article:
Integrative genome-scale metabolic analysis of Vibrio vulnificus for drug targeting and discovery
Hyun Uk Kim, Soo Young Kim, Haeyoung Jeong, Tae Yong Kim, Jae Jong Kim, Hyon E Choy, Kyu Yang Yi, Joon Haeng Rhee, and Sang Yup Lee. Molecular Systems Biology 7:460 Jan 2011 doi: 10.1038/msb.2010.115

Abstract:
Although the genomes of many microbial pathogens have been studied to help identify effective drug targets and novel drugs, such efforts have not yet reached full fruition. In this study, we report a systems biological approach that efficiently utilizes genomic information for drug targeting and discovery, and apply this approach to the opportunistic pathogen Vibrio vulnificus CMCP6. First, we partially re-sequenced and fully re-annotated the V. vulnificus CMCP6 genome, and accordingly reconstructed its genome-scale metabolic network, VvuMBEL943. The validated network model was employed to systematically predict drug targets using the concept of metabolite essentiality, along with additional filtering criteria. Target genes encoding enzymes that interact with the five essential metabolites finally selected were experimentally validated. These five essential metabolites are critical to the survival of the cell, and hence were used to guide the cost-effective selection of chemical analogs, which were then screened for antimicrobial activity in a whole-cell assay. This approach is expected to help fill the existing gap between genomics and drug discovery.

This metabolic network model has been thoroughly validated by the authors. VvuMBEL943 is a stoichiometric model that contains the metabolic information of the microbial pathogen, Vibrio vulnificus CMCP6, at genome-scale. The SBML version was generated by Hyun Uk Kim using MetaFluxNet.

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