Elimination of thermodynamically infeasible loops in steady-state metabolic models.

ABSTRACT: The constraint-based reconstruction and analysis (COBRA) framework has been widely used to study steady-state flux solutions in genome-scale metabolic networks. One shortcoming of current COBRA methods is the possible violation of the loop law in the computed steady-state flux solutions. The loop law is analogous to Kirchhoff's second law for electric circuits, and states that at steady state there can be no net flux around a closed network cycle. Although the consequences of the loop law have been known for years, it has been computationally difficult to work with. Therefore, the resulting loop-law constraints have been overlooked. Here, we present a general mixed integer programming approach called loopless COBRA (ll-COBRA), which can be used to eliminate all steady-state flux solutions

SUBMITTER: Schellenberger J 

PROVIDER: S-EPMC3030201 | biostudies-literature | 2011 Feb

REPOSITORIES: biostudies-literature