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In Silico Design Strategies for the Production of Target Chemical Compounds Using Iterative Single-Level Linear Programming Problems

The optimization of metabolic reaction modifications for the production of target compounds is a complex computational problem whose execution time increases exponentially with the number of metabolic reactions. Therefore, practical technologies are needed to identify reaction deletion combinations...

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Detalles Bibliográficos
Autores principales: Shirai, Tomokazu, Kondo, Akihiko
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9138359/
https://www.ncbi.nlm.nih.gov/pubmed/35625545
http://dx.doi.org/10.3390/biom12050620
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author Shirai, Tomokazu
Kondo, Akihiko
author_facet Shirai, Tomokazu
Kondo, Akihiko
author_sort Shirai, Tomokazu
collection PubMed
description The optimization of metabolic reaction modifications for the production of target compounds is a complex computational problem whose execution time increases exponentially with the number of metabolic reactions. Therefore, practical technologies are needed to identify reaction deletion combinations to minimize computing times and promote the production of target compounds by modifying intracellular metabolism. In this paper, a practical metabolic design technology named AERITH is proposed for high-throughput target compound production. This method can optimize the production of compounds of interest while maximizing cell growth. With this approach, an appropriate combination of metabolic reaction deletions can be identified by solving a simple linear programming problem. Using a standard CPU, the computation time could be as low as 1 min per compound, and the system can even handle large metabolic models. AERITH was implemented in MATLAB and is freely available for non-profit use.
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spelling pubmed-91383592022-05-28 In Silico Design Strategies for the Production of Target Chemical Compounds Using Iterative Single-Level Linear Programming Problems Shirai, Tomokazu Kondo, Akihiko Biomolecules Article The optimization of metabolic reaction modifications for the production of target compounds is a complex computational problem whose execution time increases exponentially with the number of metabolic reactions. Therefore, practical technologies are needed to identify reaction deletion combinations to minimize computing times and promote the production of target compounds by modifying intracellular metabolism. In this paper, a practical metabolic design technology named AERITH is proposed for high-throughput target compound production. This method can optimize the production of compounds of interest while maximizing cell growth. With this approach, an appropriate combination of metabolic reaction deletions can be identified by solving a simple linear programming problem. Using a standard CPU, the computation time could be as low as 1 min per compound, and the system can even handle large metabolic models. AERITH was implemented in MATLAB and is freely available for non-profit use. MDPI 2022-04-21 /pmc/articles/PMC9138359/ /pubmed/35625545 http://dx.doi.org/10.3390/biom12050620 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Shirai, Tomokazu
Kondo, Akihiko
In Silico Design Strategies for the Production of Target Chemical Compounds Using Iterative Single-Level Linear Programming Problems
title In Silico Design Strategies for the Production of Target Chemical Compounds Using Iterative Single-Level Linear Programming Problems
title_full In Silico Design Strategies for the Production of Target Chemical Compounds Using Iterative Single-Level Linear Programming Problems
title_fullStr In Silico Design Strategies for the Production of Target Chemical Compounds Using Iterative Single-Level Linear Programming Problems
title_full_unstemmed In Silico Design Strategies for the Production of Target Chemical Compounds Using Iterative Single-Level Linear Programming Problems
title_short In Silico Design Strategies for the Production of Target Chemical Compounds Using Iterative Single-Level Linear Programming Problems
title_sort in silico design strategies for the production of target chemical compounds using iterative single-level linear programming problems
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9138359/
https://www.ncbi.nlm.nih.gov/pubmed/35625545
http://dx.doi.org/10.3390/biom12050620
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