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

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

doi:10.1016/j.synbio.2017.11.002

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

Journal Article · Tue Nov 14 23:00:00 EST 2017 · Synthetic and Systems Biotechnology

DOI: https://doi.org/10.1016/j.synbio.2017.11.002 · OSTI ID:1629793

^[1]; Dash, Satyakam ^[2]; Ng, Chiam Yu ^[2]; Maranas, Costas D. ^[2]

Pennsylvania State University, University Park, PA (United States); DOE/OSTI
Pennsylvania State University, University Park, PA (United States)

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.

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Research Organization:: Pennsylvania State University, University Park, PA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES). Chemical Sciences, Geosciences & Biosciences Division; National Science Foundation (NSF)

Grant/Contract Number:: SC0008091

OSTI ID:: 1629793

Journal Information:: Synthetic and Systems Biotechnology, Journal Name: Synthetic and Systems Biotechnology Journal Issue: 4 Vol. 2; ISSN 2405-805X

Publisher:: ElsevierCopyright Statement

Country of Publication:: United States

Language:: English

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