title: FastPros: screening of reaction knockout strategies for metabolic engineering.
abstract: BACKGROUND
  Although constraint-based flux analysis of knockout strains has facilitated the production of desirable metabolites in microbes, current screening methods have placed a limitation on the number knockouts that can be simultaneously analyzed.
  
  
  RESULTS
  Here, we propose a novel screening method named FastPros. In this method, the potential of a given reaction knockout for production of a specific metabolite is evaluated by shadow pricing of the constraint in the flux balance analysis, which generates a screening score to obtain candidate knockout sets. To evaluate the performance of FastPros, we screened knockout sets to produce each metabolite in the entire Escherichia coli metabolic network. We found that 75% of these metabolites could be produced under biomass maximization conditions by adding up to 25 reaction knockouts. Furthermore, we demonstrated that using FastPros in tandem with another screening method, OptKnock, could further improve target metabolite productivity.
  
  
  METHODS
  Source code is freely available at http://www-shimizu.ist.osaka-u.ac.jp/shimizu_lab/FastPros/, implemented in MATLAB and COBRA toolbox.
authors.affiliation: Department of Bioinformatic Engineering, Graduate School of Information Science and Technology, Osaka University, 1-5 Yamadaoka, Suita, Osaka 565-0871 and Quantitative Biology Center (QBiC), RIKEN, 6-2-3 Furuedai, Suita, Osaka 565-0874, Japan.
authors.forename: Satoshi
authors.initials: S
authors.lastname: Ohno
authors.forename: Hiroshi
authors.initials: H
authors.lastname: Shimizu
authors.forename: Chikara
authors.initials: C
authors.lastname: Furusawa
mesh_terms: D000465:Algorithms; D016000:Cluster Analysis; D004926:Escherichia coli / Q000235:genetics / Q000378:metabolism*; D016680:Genome, Bacterial; D060847:Metabolic Engineering / Q000379:methods*; D053858:Metabolic Networks and Pathways