Grid-based computational methods for the design of constraint-based parsimonious chemical reaction networks to simulate metabolite production: GridProd

BMC Bioinformatics
Takeyuki Tamura

Abstract

Constraint-based metabolic flux analysis of knockout strategies is an efficient method to simulate the production of useful metabolites in microbes. Owing to the recent development of technologies for artificial DNA synthesis, it may become important in the near future to mathematically design minimum metabolic networks to simulate metabolite production. We have developed a computational method where parsimonious metabolic flux distribution is computed for designated constraints on growth and production rates which are represented by grids. When the growth rate of this obtained parsimonious metabolic network is maximized, higher production rates compared to those noted using existing methods are observed for many target metabolites. The set of reactions used in this parsimonious flux distribution consists of reactions included in the original genome scale model iAF1260. The computational experiments show that the grid size affects the obtained production rates. Under the conditions that the growth rate is maximized and the minimum cases of flux variability analysis are considered, the developed method produced more than 90% of metabolites, while the existing methods produced less than 50%. Mathematical explanations using exampl...Continue Reading

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Software Mentioned

MATLAB
OptReg
GDLS
Gurobi
OptKnock
Redirector
IdealKnock GridProd
Genetic Design through Local Search ( GDLS
SimOptStrain
etha

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