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novoPathFinder: a w...
novoPathFinder: a webserver of designing novel-pathway with integrating GEM-model
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- Ding, Shaozhen (författare)
- Chinese Academy of Sciences
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- Tian, Yu (författare)
- Wuhan University of Technology
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- Cai, Pengli (författare)
- Chinese Academy of Sciences
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- Zhang, Dachuan (författare)
- Chinese Academy of Sciences
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- Cheng, Xingxiang (författare)
- Chinese Academy of Sciences
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- Sun, Dandan (författare)
- Chinese Academy of Sciences
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- Yuan, Le, 1994 (författare)
- Chalmers tekniska högskola,Chalmers University of Technology
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Chen, Junni (författare)
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Tu, Weizhong (författare)
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- Wei, Dong Qing (författare)
- Shanghai Jiao Tong University
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- Hu, Qian Nan (författare)
- Chinese Academy of Sciences
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(creator_code:org_t)
- 2020-04-20
- 2020
- Engelska.
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Ingår i: Nucleic Acids Research. - : Oxford University Press (OUP). - 0305-1048 .- 1362-4962. ; 48:W1, s. W477-W487
- Relaterad länk:
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https://research.cha... (primary) (free)
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https://doi.org/10.1...
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https://doi.org/10.1...
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https://research.cha...
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Abstract
Ämnesord
Stäng
- To increase the number of value-added chemicals that can be produced by metabolic engineering and synthetic biology, constructing metabolic space with novel reactions/pathways is crucial. However, with the large number of reactions that existed in the metabolic space and complicated metabolisms within hosts, identifying novel pathways linking two molecules or heterologous pathways when engineering a host to produce a target molecule is an arduous task. Hence, we built a user-friendly web server, novoPathFinder, which has several features: (i) enumerate novel pathways between two specified molecules without considering hosts; (ii) construct heterologous pathways with known or putative reactions for producing target molecule within Escherichia coli or yeast without giving precursor; (iii) estimate novel pathways with considering several categories, including enzyme promiscuity, Synthetic Complex Score (SCScore) and LD50 of intermediates, overall stoichiometric conversions, pathway length, theoretical yields and thermodynamic feasibility. According to the results, novoPathFinder is more capable to recover experimentally validated pathways when comparing other rule-based web server tools. Besides, more efficient pathways with novel reactions could also be retrieved for further experimental exploration. novoPathFinder is available at http://design.rxnfinder.org/novopathfinder/.
Ämnesord
- NATURVETENSKAP -- Kemi -- Teoretisk kemi (hsv//swe)
- NATURAL SCIENCES -- Chemical Sciences -- Theoretical Chemistry (hsv//eng)
- TEKNIK OCH TEKNOLOGIER -- Industriell bioteknik -- Biokatalys och enzymteknik (hsv//swe)
- ENGINEERING AND TECHNOLOGY -- Industrial Biotechnology -- Biocatalysis and Enzyme Technology (hsv//eng)
- NATURVETENSKAP -- Kemi -- Organisk kemi (hsv//swe)
- NATURAL SCIENCES -- Chemical Sciences -- Organic Chemistry (hsv//eng)
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- ref (ämneskategori)
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Till lärosätets databas
- Av författaren/redakt...
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Ding, Shaozhen
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Tian, Yu
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Cai, Pengli
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Zhang, Dachuan
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Cheng, Xingxiang
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Sun, Dandan
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visa fler...
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Yuan, Le, 1994
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Chen, Junni
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Tu, Weizhong
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Wei, Dong Qing
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Hu, Qian Nan
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visa färre...
- Om ämnet
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- NATURVETENSKAP
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NATURVETENSKAP
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och Kemi
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och Teoretisk kemi
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- TEKNIK OCH TEKNOLOGIER
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TEKNIK OCH TEKNO ...
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och Industriell biot ...
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och Biokatalys och e ...
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- NATURVETENSKAP
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NATURVETENSKAP
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och Kemi
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och Organisk kemi
- Artiklar i publikationen
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Nucleic Acids Re ...
- Av lärosätet
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Chalmers tekniska högskola