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Optknock specifications

Information


Unique identifier OMICS_06452
Name Optknock
Software type Framework/Library
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability Stable
Maintained Yes

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Publication for Optknock

Optknock in publications

 (65)
PMCID: 5790215
PMID: 29381705
DOI: 10.1371/journal.pone.0189144

[…] the presence of such a degradation pathway in vivo, which we do not consider in silico, might be the cause behind the overestimation of the ethanol production flux by our model., we used the optknock algorithm to predict both single and double reaction knockouts for maximizing succinate production in the minimal am3 medium while restraining the growth to be at least 0.1 gdcw hr-1 […]

PMCID: 5725212
PMID: 29255672
DOI: 10.1016/j.meteno.2017.11.001

[…] the pan-propionibacterium gem to design genetic modification strategies. because the production of propionic acid is already growth-coupled, classic growth-coupling strain design algorithms such as optknock () favour sub-optimal strategies that limit energy generation, leaving cells more susceptible to acid stress. given the depletion of the ph gradient is regarded as a major mechanism […]

PMCID: 5662904
PMID: 29123506
DOI: 10.3389/fmicb.2017.02060

[…] through gene knock-out (; ; ), upregulation/downregulation (; ; ; ), and heterologous gene expression of foreign pathways (; table )., the first computational-aided strain design program, optknock, was developed for simulating gene deletion by employing a bi-level optimization program to seek reaction knock-out targets that would yield overproduction of a desired compound […]

PMCID: 5629566
PMID: 28984191
DOI: 10.1186/s12864-017-4025-7

[…] of existing bi-level methods for strain optimization under uncertainty and non-cooperative environment. more importantly, we propose new pessimistic optimization formulations: p-room and p-optknock, aiming to derive robust mutants with the desired overproduction under two different mutant cell survival models: (1) room assuming mutants have the minimum changes in reaction fluxes […]

PMCID: 5539140
PMID: 28824562
DOI: 10.3389/fmicb.2017.01428

[…] in the chemostat experiments, we predicted growth rate values of 0.042 h−1; which demonstrated the validity and consistency of the modified metabolic model m_imk1208. we then used the computational optknock framework (burgard et al., ) in order to predict possible mutations leading to an increase in carbon fluxes toward tag biosynthesis. optknock was performed with both models with the output […]


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Optknock institution(s)
Department of Chemical Engineering, The Pennsylvania State University, University Park, PA, USA

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