Computational tools for the synthetic design of biochemical pathways

Marnix H. Medema; Renske Van Raaphorst; Eriko Takano; Rainer Breitling

doi:10.1038/nrmicro2717

Computational tools for the synthetic design of biochemical pathways

Marnix H. Medema, Renske Van Raaphorst, Eriko Takano, Rainer Breitling

Research output: Contribution to journal › Article › peer-review

Abstract

As the field of synthetic biology is developing, the prospects for de novo design of biosynthetic pathways are becoming more and more realistic. Hence, there is an increasing need for computational tools that can support these efforts. A range of algorithms has been developed that can be used to identify all possible metabolic pathways and their corresponding enzymatic parts. These can then be ranked according to various properties and modelled in an organism-specific context. Finally, design software can aid the biologist in the integration of a selected pathway into smartly regulated transcriptional units. Here, we review key existing tools and offer suggestions for how informatics can help to shape the future of synthetic microbiology. © 2012 Macmillan Publishers Limited. All rights reserved.

Original language	English
Pages (from-to)	191-202
Number of pages	11
Journal	Nature Reviews Microbiology
Volume	10
Issue number	3
DOIs	https://doi.org/10.1038/nrmicro2717
Publication status	Published - Mar 2012

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10.1038/nrmicro2717

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title = "Computational tools for the synthetic design of biochemical pathways",

abstract = "As the field of synthetic biology is developing, the prospects for de novo design of biosynthetic pathways are becoming more and more realistic. Hence, there is an increasing need for computational tools that can support these efforts. A range of algorithms has been developed that can be used to identify all possible metabolic pathways and their corresponding enzymatic parts. These can then be ranked according to various properties and modelled in an organism-specific context. Finally, design software can aid the biologist in the integration of a selected pathway into smartly regulated transcriptional units. Here, we review key existing tools and offer suggestions for how informatics can help to shape the future of synthetic microbiology. {\textcopyright} 2012 Macmillan Publishers Limited. All rights reserved.",

author = "Medema, {Marnix H.} and {Van Raaphorst}, Renske and Eriko Takano and Rainer Breitling",

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Computational tools for the synthetic design of biochemical pathways

Abstract

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