ArticlePloS one2014
Combining chemoinformatics with bioinformatics: in silico prediction of bacterial flavor-forming pathways by a chemical systems biology approach "reverse pathway engineering".
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers, 1 of them a synthesis that pooled it.
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Who cites it
13 citing papers in PubMed, 1 synthesis or guideline pooled it.
- The role of fermented foods in managing food allergies in children and adults: a systematic review.Frontiers in nutrition · 2025Pooled it
- From Charcuterie to Plant-Based: HarnessingFoods (Basel, Switzerland) · 2026Article
- Decoding the Aroma Gap: Sensomics-Based Characterization of Key Odorants in the Plant-Based Egg and Chicken Egg.Journal of agricultural and food chemistry · 2025Article
- Molecular similarity: Theory, applications, and perspectives.Artificial intelligence chemistry · 2024Article
- Effects of pH and Osmotic Changes on the Metabolic Expressions ofMetabolites · 2022Article
- PyMiner: A method for metabolic pathway design based on the uniform similarity of substrate-product pairs and conditional search.PloS one · 2022Article
- Chemistry in Times of Artificial Intelligence.Chemphyschem : a European journal of chemical physics and physical chemistry · 2020Review
- Computational Approaches to Design and Test Plant Synthetic Metabolic Pathways.Plant physiology · 2019Review
- SimCAL: a flexible tool to compute biochemical reaction similarity.BMC bioinformatics · 2018Article
- Using bioinformatics tools for the discovery of Dengue RNA-dependent RNA polymerase inhibitors.PeerJ · 2018Article
- Molecular structures enumeration and virtual screening in the chemical space with RetroPath2.0.Journal of cheminformatics · 2017Article
- A review of computational tools for design and reconstruction of metabolic pathways.Synthetic and systems biotechnology · 2017Review
- Chemoinformatics: Achievements and Challenges, a Personal View.Molecules (Basel, Switzerland) · 2016Review
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Authors and funding
7 authors.
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Abstract
The incompleteness of genome-scale metabolic models is a major bottleneck for systems biology approaches, which are based on large numbers of metabolites as identified and quantified by metabolomics. Many of the revealed secondary metabolites and/or their derivatives, such as flavor compounds, are non-essential in metabolism, and many of their synthesis pathways are unknown. In this study, we describe a novel approach, Reverse Pathway Engineering (RPE), which combines chemoinformatics and bioinformatics analyses, to predict the "missing links" between compounds of interest and their possible metabolic precursors by providing plausible chemical and/or enzymatic reactions. We demonstrate the added-value of the approach by using flavor-forming pathways in lactic acid bacteria (LAB) as an example. Established metabolic routes leading to the formation of flavor compounds from leucine were successfully replicated. Novel reactions involved in flavor formation, i.e. the conversion of alpha-hydroxy-isocaproate to 3-methylbutanoic acid and the synthesis of dimethyl sulfide, as well as the involved enzymes were successfully predicted. These new insights into the flavor-formation mechanisms in LAB can have a significant impact on improving the control of aroma formation in fermented food products. Since the input reaction databases and compounds are highly flexible, the RPE approach can be easily extended to a broad spectrum of applications, amongst others health/disease biomarker discovery as well as synthetic biology.
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