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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 citations

 (85)
library_books

Alignment of microbial fitness with engineered product formation: obligatory coupling between acetate production and photoautotrophic growth

2018
Biotechnol Biofuels
PMCID: 5809919
PMID: 29456625
DOI: 10.1186/s13068-018-1037-8

[…] we want to find whether there are gene deletions that completely disrupt the re-utilization of a target compound, and if so, which one(s). This is achieved using an in-house Python implementation of OptKnock [], extended for gene deletions []. The user can choose the maximum number of permitted deletions such that it satisfies experimental limitations. OptKnock is very useful to identify the gene […]

library_books

Prediction of reaction knockouts to maximize succinate production by Actinobacillus succinogenes

2018
PLoS One
PMCID: 5790215
PMID: 29381705
DOI: 10.1371/journal.pone.0189144

[…] 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 and the […]

library_books

Genome scale model guided design of Propionibacterium for enhanced propionic acid production

2017
Metab Eng Com
PMCID: 5725212
PMID: 29255672
DOI: 10.1016/j.meteno.2017.11.001

[…] Initial genetic engineering targets were designed using the OptKnock algorithm. Three key strategies were identified to improve flux towards propionate. The first strategy involved reducing the total energy available to the organism by knocking out the energy […]

library_books

Challenges and Advances for Genetic Engineering of Non model Bacteria and Uses in Consolidated Bioprocessing

2017
Front Microbiol
PMCID: 5662904
PMID: 29123506
DOI: 10.3389/fmicb.2017.02060

[…] intervention 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 while maintai […]

library_books

Robust mutant strain design by pessimistic optimization

2017
BMC Genomics
PMCID: 5629566
PMID: 28984191
DOI: 10.1186/s12864-017-4025-7

[…] timization methods on a core E. coli metabolic network [] when the outer- and inner-level decision makers are not cooperative. We then test our robust strain optimization methods, namely P-ROOM and P-OptKnock, derived in the “” section, on the core network and a large E. coli metabolic network, iAF1260 [], for overproduction of Succinate. The models are optimized using the MILP solver CPLEX 12.6.3 […]

library_books

The International Conference on Intelligent Biology and Medicine (ICIBM) 2016: summary and innovation in genomics

2017
BMC Genomics
PMCID: 5629612
PMID: 28984207
DOI: 10.1186/s12864-017-4018-6

[…] ness of existing bi-level methods for strain optimization under uncertainty and non-cooperative environment. Specifically, the authors proposed new pessimistic optimization formulations: P-ROOM and P-OptKnock, aiming to derive robust mutants with the desired overproduction under two different existing mutant cell survival models, ROOM and OptKnock. Their pessimistic strain optimization methods cou […]

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

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