ArticleBiotechnology and bioengineering2009
Computational framework for predictive biodegradation.
Article in Biotechnology and bioengineering, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
25 citing papers in PubMed.
- Accurately predicting enzyme functions through geometric graph learning on ESMFold-predicted structures.Nature communications · 2024Article
- NICEdrug.ch, a workflow for rational drug design and systems-level analysis of drug metabolism.eLife · 2021Article
- Methodological Advances to Study Contaminant Biotransformation: New Prospects for Understanding and Reducing Environmental Persistence?ACS ES&T water · 2021Review
- Analysis of metabolic network disruption in engineered microbial hosts due to enzyme promiscuity.Metabolic engineering communications · 2021Article
- Stability Analysis of a Signaling Circuit with Dual Species of GTPase Switches.Bulletin of mathematical biology · 2021Article
- The ever-expanding limits of enzyme catalysis and biodegradation: polyaromatic, polychlorinated, polyfluorinated, and polymeric compounds.The Biochemical journal · 2020Review
- Updated ATLAS of Biochemistry with New Metabolites and Improved Enzyme Prediction Power.ACS synthetic biology · 2020Article
- Omics Approaches to Pesticide Biodegradation.Current microbiology · 2020Review
- Deep learning enables high-quality and high-throughput prediction of enzyme commission numbers.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Pathway design using de novo steps through uncharted biochemical spaces.Nature communications · 2018Article
- Seven microbial bio-processes to help the planet.Microbial biotechnology · 2017Article
- Integrated Framework for Identifying Toxic Transformation Products in Complex Environmental Mixtures.Environmental science & technology letters · 2017Article
- The Protein Cost of Metabolic Fluxes: Prediction from Enzymatic Rate Laws and Cost Minimization.PLoS computational biology · 2016Article
- enviPath--The environmental contaminant biotransformation pathway resource.Nucleic acids research · 2016Article
- Antihypertensive drugs metabolism: an update to pharmacokinetic profiles and computational approaches.Current pharmaceutical design · 2015Review
- A systems approach to predict oncometabolites via context-specific genome-scale metabolic networks.PLoS computational biology · 2014Article
- A review of metabolic and enzymatic engineering strategies for designing and optimizing performance of microbial cell factories.Computational and structural biotechnology journal · 2014Review
- Computational evaluation of factors governing catalytic 2-keto acid decarboxylation.Journal of molecular modeling · 2014Article
- The path of anti-tuberculosis drugs: from blood to lesions to mycobacterial cells.Nature reviews. Microbiology · 2014Review
- Integration of bioinformatics to biodegradation.Biological procedures online · 2014Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
As increasing amounts of anthropogenic chemicals are released into the environment, it is vital to human health and the preservation of ecosystems to evaluate the fate of these chemicals in the environment. It is useful to predict whether a particular compound is biodegradable and if alternate routes can be engineered for compounds already known to be biodegradable. In this work, we describe a computational framework (called BNICE) that can be used for the prediction of novel biodegradation pathways of xenobiotics. The framework was applied to 4-chlorobiphenyl, phenanthrene, gamma-hexachlorocyclohexane, and 1,2,4-trichlorobenzene, compounds representing various classes of xenobiotics with known biodegradation routes. BNICE reproduced the proposed biodegradation routes found experimentally, and in addition, it expanded the biodegradation reaction networks through the generation of novel compounds and reactions. The novel reactions involved in the biodegradation of 1,2,4-trichlorobenzene were studied in depth, where pathway and thermodynamic analyses were performed. This work demonstrates that BNICE can be applied to generate novel pathways to degrade xenobiotic compounds that are thermodynamically feasible alternatives to known biodegradation routes and attractive targets for metabolic engineering.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.