A review of computational tools for design and reconstruction of metabolic pathways

Lin Wang, Satyakam Dash, Chiam Yu Ng, Costas D. Maranas

Research output: Contribution to journalReview article

22 Citations (Scopus)

Abstract

Metabolic pathways reflect an organism's chemical repertoire and hence their elucidation and design have been a primary goal in metabolic engineering. Various computational methods have been developed to design novel metabolic pathways while taking into account several prerequisites such as pathway stoichiometry, thermodynamics, host compatibility, and enzyme availability. The choice of the method is often determined by the nature of the metabolites of interest and preferred host organism, along with computational complexity and availability of software tools. In this paper, we review different computational approaches used to design metabolic pathways based on the reaction network representation of the database (i.e., graph or stoichiometric matrix) and the search algorithm (i.e., graph search, flux balance analysis, or retrosynthetic search). We also put forth a systematic workflow that can be implemented in projects requiring pathway design and highlight current limitations and obstacles in computational pathway design.

Original languageEnglish (US)
Pages (from-to)243-252
Number of pages10
JournalSynthetic and Systems Biotechnology
Volume2
Issue number4
DOIs
StatePublished - Dec 1 2017

Fingerprint

Metabolic Networks and Pathways
Metabolic Engineering
Workflow
Thermodynamics
Availability
Metabolic engineering
Software
Databases
Metabolites
Computational methods
Stoichiometry
Enzymes
Computational complexity
Fluxes

All Science Journal Classification (ASJC) codes

  • Structural Biology
  • Biomedical Engineering
  • Applied Microbiology and Biotechnology
  • Genetics

Cite this

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A review of computational tools for design and reconstruction of metabolic pathways. / Wang, Lin; Dash, Satyakam; Ng, Chiam Yu; Maranas, Costas D.

In: Synthetic and Systems Biotechnology, Vol. 2, No. 4, 01.12.2017, p. 243-252.

Research output: Contribution to journalReview article

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