ArticleNucleic acids research2020
novoPathFinder: a webserver of designing novel-pathway with integrating GEM-model.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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Who cites it
11 citing papers in PubMed.
- A Comprehensive Review: Current Strategies for Detoxification of Deoxynivalenol in Feedstuffs for Pigs.Animals : an open access journal from MDPI · 2025Review
- From reactants to products: computational methods for biosynthetic pathway design.Synthetic and systems biotechnology · 2025Review
- novoStoic2.0: An integrated framework for pathway synthesis, thermodynamic evaluation, and enzyme selection.PLoS computational biology · 2025Article
- Integrated pathway mining and selection of an artificial CYP79-mediated bypass to improve benzylisoquinoline alkaloid biosynthesis.Microbial cell factories · 2024Article
- MCF2Chem: A manually curated knowledge base of biosynthetic compound production.Biotechnology for biofuels and bioproducts · 2023Article
- enviRule: an end-to-end system for automatic extraction of reaction patterns from environmental contaminant biotransformation pathways.Bioinformatics (Oxford, England) · 2023Article
- Pickaxe: a Python library for the prediction of novel metabolic reactions.BMC bioinformatics · 2023Article
- Design and Construction of Artificial Biological Systems for One-Carbon Utilization.Biodesign research · 2023Review
- SelenzymeRF: updated enzyme suggestion software for unbalanced biochemical reactions.Computational and structural biotechnology journal · 2023Article
- Expanding biochemical knowledge and illuminating metabolic dark matter with ATLASx.Nature communications · 2022Article
- A computational workflow for the expansion of heterologous biosynthetic pathways to natural product derivatives.Nature communications · 2021Article
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Authors and funding
11 authors.
Funding
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Abstract
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/.
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