Fig. 5
From: Optimal knockout strategies in genome-scale metabolic networks using particle swarm optimization
Design for a genome-scale E. coli model. E. coli was designed for enhanced ethanol production using the genome-scale iAF1260 model. For comparison, designs obtained using OptKnock and RobustKnock are also presented. The design using PSOMCS guarantees a minimal ethanol yield of 0.9, in contrast this is 0 for both RobustKnock and OptKnock. All designs have a maximum biomass production rate greater than 0.01 with the one for PSOMCS being comparatively lower. The maximum yield for all the designs is 2. The given plots have been generated by using FVA on the iAF1260 model while considering the respective knockouts produced by each method. The FBA solution space at maximum growth is highlighted, with crosses indicating the maximum and squares the minimum ethanol yield. All designs involve 5 knockouts - (R_ACALD R_GLUDy R_Htex R_PGI R_TKT2) for PSOMCS, (R_ACALD R_H2tex R_PHEt2rpp R_PPKr R_TYRtex) for OptKnock and (R_ACKr R_F6PA R_FBA R_GLCptspp R_PGCD) for RobustKnock