ArticleJournal of cheminformatics2024
Advancements in biotransformation pathway prediction: enhancements, datasets, and novel functionalities in enviPath.
Article in Journal of cheminformatics, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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Who cites it
12 citing papers in PubMed.
- Advancing the Discovery of Emerging Contaminants: A Leap in Technology and Data.Environmental science & technology · 2026Review
- Predicting enzyme-compound associations for enzyme-catalysed reactions.Journal of cheminformatics · 2026Article
- Persistence Assessment of Chemicals: Trajectories toward New Approach Methodologies (P-NAMs).Environmental science & technology · 2026Review
- Insights into the biodegradation of two persistent fluorinated fungicides by coupling metabolic modelling with metaproteogenomics.Scientific reports · 2026Article
- Diagnosing soil bioremediation failure: evidence-weighted pathways from mechanism to field closure.Frontiers in bioengineering and biotechnology · 2026Review
- FAIR and Effective Communication of Data on Chemical Contaminant Biotransformation in the Environment.Environmental science & technology letters · 2025Review
- Large-scale generation of in silico based spectral libraries to annotate dark chemical space features in non-target analysis.Analytical and bioanalytical chemistry · 2025Article
- Predicting Micropollutant Removal in Wastewater Treatment Based on Molecular Structure: Benchmark Data and Models.Environmental science & technology · 2025Article
- Biotransformation Dynamics and Products of Cyanobacterial Secondary Metabolites in Surface Waters.Environmental science & technology · 2025Article
- Review
- Characterizing cyanopeptides and transformation products in freshwater: integrating targeted, suspect, and non-targeted analysis with in silico modeling.Analytical and bioanalytical chemistry · 2025Article
- Predictive modeling of biodegradation pathways using transformer architectures.Journal of cheminformatics · 2025Article
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Authors and funding
8 authors.
Funding
Abstract
enviPath is a widely used database and prediction system for microbial biotransformation pathways of primarily xenobiotic compounds. Data and prediction system are freely available both via a web interface and a public REST API. Since its initial release in 2016, we extended the data available in enviPath and improved the performance of the prediction system and usability of the overall system. We now provide three diverse data sets, covering microbial biotransformation in different environments and under different experimental conditions. This also enabled developing a pathway prediction model that is applicable to a more diverse set of chemicals. In the prediction engine, we implemented a new evaluation tailored towards pathway prediction, which returns a more honest and holistic view on the performance. We also implemented a novel applicability domain algorithm, which allows the user to estimate how well the model will perform on their data. Finally, we improved the implementation to speed up the overall system and provide new functionality via a plugin system. SCIENTIFIC CONTRIBUTION: The main scientific contributions are the development of a pathway prediction model applicable to diverse chemicals, a specialized evaluation method for holistic performance assessment, and a novel applicability domain algorithm for user-specific performance estimation. The introduction of two new data sets, and the creation of links to EC classes make enviPath a unique resource in microbial biotransformation research.
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Registered trials
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