Additional file 18.
Ranked predicted essential reactions. Knock-outs were simulated with a simple FBA approach neglecting gene expression information. No assumptions were made about the cellular environment and nutrient uptake was not restricted, since such information is not available for all stages. Successively reactions were constrained to carry no flux, while the network was forced to produce all metabolites that are assumed to be essential during any developmental stage (all metabolites listed in Additional file 9). If no solution could be found to this problem the reaction was assumed to be essential. The resulting set of indispensable reactions, which are assigned to genes and not covered by our gold standard set of experimentally validated essential enzymes, is listed here. Reactions are ranked according to a score that is derived as follows: two points if corresponding genes are not homologous to human genes, an additional point if the reaction is targeted in any other organism (according to the SuperTarget database), and another additional point if the reaction is active during all parasitic life cycle stages, which makes respective drugs applicable for prophylaxis as well as disease treatment.
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Huthmacher et al. BMC Systems Biology 2010 4:120 doi:10.1186/1752-0509-4-120