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BMC Systems Biology

, 6:140

Methods, software and technology


BackgroundConstraint-based modeling is increasingly employed for metabolic network analysis. Its underlying assumption is that natural metabolic phenotypes can be predicted by adding physicochemical constraints to remove unrealistic metabolic flux solutions. The loopless-COBRA approach provides an additional constraint that eliminates thermodynamically infeasible internal cycles or loops from the space of solutions. This allows the prediction of flux solutions that are more consistent with experimental data. However, it is not clear if this approach over-constrains the models by removing non-loop solutions as well.

ResultsHere we apply Gordan’s theorem from linear algebra to prove for the first time that the constraints added in loopless-COBRA do not over-constrain the problem beyond the elimination of the loops themselves.

ConclusionsThe loopless-COBRA constraints can be reliably applied. Furthermore, this proof may be adapted to evaluate the theoretical soundness for other methods in constraint-based modeling.

KeywordsThermodynamics Gordan’s theorem Metabolism Electronic supplementary materialThe online version of this article doi:10.1186-1752-0509-6-140 contains supplementary material, which is available to authorized users.

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Autor: Elad Noor - Nathan E Lewis - Ron Milo

Fuente: https://link.springer.com/

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