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dc.contributor.authorMotwalli, Olaa Amin
dc.contributor.authorUludag, Mahmut
dc.contributor.authorMijakovic, Ivan
dc.contributor.authorAlazmi, Meshari
dc.contributor.authorBajic, Vladimir B.
dc.contributor.authorGojobori, Takashi
dc.contributor.authorGao, Xin
dc.contributor.authorEssack, Magbubah
dc.date.accessioned2020-11-19T10:41:06Z
dc.date.available2020-11-19T10:41:06Z
dc.date.issued2020-11-16
dc.date.submitted2020-02-02
dc.identifier.citationMotwalli, O., Uludag, M., Mijakovic, I., Alazmi, M., Bajic, V. B., Gojobori, T., … Essack, M. (2020). PATHcre8: A Tool That Facilitates the Searching for Heterologous Biosynthetic Routes. ACS Synthetic Biology. doi:10.1021/acssynbio.0c00058
dc.identifier.issn2161-5063
dc.identifier.issn2161-5063
dc.identifier.pmid33198455
dc.identifier.doi10.1021/acssynbio.0c00058
dc.identifier.urihttp://hdl.handle.net/10754/666037
dc.description.abstractDeveloping computational tools that can facilitate the rational design of cell factories producing desired products at increased yields is challenging, as the tool needs to take into account that the preferred host organism usually has compounds that are consumed by competing reactions that reduce the yield of the desired product. On the other hand, the preferred host organisms may not have the native metabolic reactions needed to produce the compound of interest; thus, the computational tool needs to identify the metabolic reactions that will most efficiently produce the desired product. In this regard, we developed the generic tool PATHcre8 to facilitate an optimized search for heterologous biosynthetic pathway routes. PATHcre8 finds and ranks biosynthesis routes in a large number of organisms, including Cyanobacteria. The tool ranks the pathways based on feature scores that reflect reaction thermodynamics, the potentially toxic products in the pathway (compound toxicity), intermediate products in the pathway consumed by competing reactions (product consumption), and host-specific information such as enzyme copy number. A comparison with several other similar tools shows that PATHcre8 is more efficient in ranking functional pathways. To illustrate the effectiveness of PATHcre8, we further provide case studies focused on isoprene production and the biodegradation of cocaine. PATHcre8 is free for academic and nonprofit users and can be accessed at https://www.cbrc.kaust.edu.sa/pathcre8/.
dc.description.sponsorshipThis work has been supported by the King Abdullah University of Science and Technology (KAUST) Base Research Fund BAS/1/1606-01-01, BAS/1/1059-01-01, BAS/1/1624-01-01, as well as through the Awards No. FCC/1/1976-02-01, FCC/1/1976-17-01, FCC/1/1976-16-01, and FCC/1/1976-26-01 from the KAUST Office of Sponsored Research (OSR). Also, the Novo Nordisk Foundation Grant NNF10CC1016517 awarded to IM.
dc.publisherAmerican Chemical Society (ACS)
dc.relation.urlhttps://pubs.acs.org/doi/10.1021/acssynbio.0c00058
dc.rightsThis document is the Accepted Manuscript version of a Published Work that appeared in final form in ACS Synthetic Biology, copyright © American Chemical Society after peer review and technical editing by the publisher. To access the final edited and published work see https://pubs.acs.org/doi/10.1021/acssynbio.0c00058.
dc.titlePATHcre8: A Tool That Facilitates the Searching for Heterologous Biosynthetic Routes
dc.typeArticle
dc.contributor.departmentApplied Mathematics and Computational Science Program
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Division
dc.contributor.departmentBioscience Program
dc.contributor.departmentComputational Bioscience Research Center (CBRC)
dc.contributor.departmentComputer Science Program
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
dc.contributor.departmentStructural and Functional Bioinformatics Group
dc.identifier.journalACS Synthetic Biology
dc.rights.embargodate2021-11-17
dc.eprint.versionPost-print
dc.contributor.institutionSaudi Electronic University (SEU), College of Computing and Informatics, Madinah 41538-53307, Kingdom of Saudi Arabia
dc.contributor.institutionChalmers University of Technology, Division of Systems & Synthetic Biology, Department of Biology and Biological Engineering, Kemivägen 10, 41296 Gothenburg, Sweden
dc.contributor.institutionNovo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, 2800 Kgs. Lyngby, Denmark
dc.contributor.institutionDepartment of Information and Computer Science, College of Computer Science and Engineering, University of Ha’il, P.O. Box 2440, Ha’il 81411, Kingdom of Saudi Arabia
kaust.personMotwalli, Olaa Amin
kaust.personUludag, Mahmut
kaust.personBajic, Vladimir B.
kaust.personGojobori, Takashi
kaust.personGojobori, Takashi
kaust.personGao, Xin
kaust.personEssack, Magbubah
kaust.grant.numberBAS/1/1059-01-01
kaust.grant.numberBAS/1/1606-01-01
kaust.grant.numberBAS/1/1624-01-01
kaust.grant.numberFCC/1/1976-02-01
kaust.grant.numberFCC/1/1976-17-01
kaust.grant.numberFCC/1/1976-26-01
refterms.dateFOA2020-11-22T13:46:58Z
kaust.acknowledged.supportUnitBase Research Fund
kaust.acknowledged.supportUnitKAUST Office of Sponsored Research (OSR)


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