OptKnock

General concept

Bacteria can metabolize and secrete a large number of compounds. Thus it is expected that gene deletions might exist that force the production of desired products as a byproduct of optimal growth. OptKnock attempts to find the sets of reaction deletions that couple a product to optimal growth, thereby allowing for design on stable production strains. Opknock uses a bi-level optimization of the desired product secretion rate subject to another objective (e.g., optimal biomass) while searching for the optimal set of reaction deletions. This can also be formulated as an MILP problem.

Items to consider when implementing

Software packages with this method

Applications of interest

Description of study and link to study:

What was learned with this method:

Relevant references

Burgard, et al.

Related methods

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