ArticleNucleic acids research2016
MRE: a web tool to suggest foreign enzymes for the biosynthesis pathway design with competing endogenous reactions in mind.
Article in Nucleic acids research, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Advances in natural product discovery: strategies, technologies, and insights.Natural products and bioprospecting · 2026Review
- Design and construction of artificial metabolic pathways for the bioproduction of useful compounds.Plant biotechnology (Tokyo, Japan) · 2024Article
- A deep learning architecture for metabolic pathway prediction.Bioinformatics (Oxford, England) · 2024Article
- COVRECON: automated integration of genome- and metabolome-scale network reconstruction and data-driven inverse modeling of metabolic interaction networks.Bioinformatics (Oxford, England) · 2023Article
- SelenzymeRF: updated enzyme suggestion software for unbalanced biochemical reactions.Computational and structural biotechnology journal · 2023Article
- Deep learning driven biosynthetic pathways navigation for natural products with BioNavi-NP.Nature communications · 2022Article
- Design, Analysis, and Implementation of a Novel Biochemical Pathway for Ethylene Glycol Production inACS synthetic biology · 2022Article
- PyMiner: A method for metabolic pathway design based on the uniform similarity of substrate-product pairs and conditional search.PloS one · 2022Article
- Synthetic Biology Advanced Natural Product Discovery.Metabolites · 2021Review
- Finding branched pathways in metabolic network via atom group tracking.PLoS computational biology · 2021Article
- CaMeRe: A Novel Tool for Inference of Cancer Metabolic Reprogramming.Frontiers in oncology · 2020Article
- Characterizing and ranking computed metabolic engineering strategies.Bioinformatics (Oxford, England) · 2019Article
- Systematic selection of chemical fingerprint features improves the Gibbs energy prediction of biochemical reactions.Bioinformatics (Oxford, England) · 2019Article
- A review of computational tools for design and reconstruction of metabolic pathways.Synthetic and systems biotechnology · 2017Review
- A review of parameters and heuristics for guiding metabolic pathfinding.Journal of cheminformatics · 2017Review
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4 authors.
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Abstract
To rationally design a productive heterologous biosynthesis system, it is essential to consider the suitability of foreign reactions for the specific endogenous metabolic infrastructure of a host. We developed a novel web server, called MRE, which, for a given pair of starting and desired compounds in a given chassis organism, ranks biosynthesis routes from the perspective of the integration of new reactions into the endogenous metabolic system. For each promising heterologous biosynthesis pathway, MRE suggests actual enzymes for foreign metabolic reactions and generates information on competing endogenous reactions for the consumption of metabolites. These unique, chassis-centered features distinguish MRE from existing pathway design tools and allow synthetic biologists to evaluate the design of their biosynthesis systems from a different angle. By using biosynthesis of a range of high-value natural products as a case study, we show that MRE is an effective tool to guide the design and optimization of heterologous biosynthesis pathways. The URL of MRE is http://www.cbrc.kaust.edu.sa/mre/.
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