ArticleNucleic acids research2014
XTMS: pathway design in an eXTended metabolic space.
Article in Nucleic acids research, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 34 papers.
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Who cites it
34 citing papers in PubMed.
- novoStoic2.0: An integrated framework for pathway synthesis, thermodynamic evaluation, and enzyme selection.PLoS computational biology · 2025Article
- Artificial Intelligence Methods and Models for Retro-Biosynthesis: A Scoping Review.ACS synthetic biology · 2024Article
- Integrated pathway mining and selection of an artificial CYP79-mediated bypass to improve benzylisoquinoline alkaloid biosynthesis.Microbial cell factories · 2024Article
- Extending PROXIMAL to predict degradation pathways of phenolic compounds in the human gut microbiota.NPJ systems biology and applications · 2024Article
- The automated Galaxy-SynBioCAD pipeline for synthetic biology design and engineering.Nature communications · 2022Article
- Enzyme Promiscuity Prediction Using Hierarchy-Informed Multi-Label Classification.Bioinformatics (Oxford, England) · 2021Article
- Improving the organization and interactivity of metabolic pathfinding with precomputed pathways.BMC bioinformatics · 2020Article
- Metabolic disassembler for understanding and predicting the biosynthetic units of natural products.BMC bioinformatics · 2019Article
- Gsmodutils: a python based framework for test-driven genome scale metabolic model development.Bioinformatics (Oxford, England) · 2019Article
- 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
- Enzyme annotation for orphan and novel reactions using knowledge of substrate reactive sites.Proceedings of the National Academy of Sciences of the United States of America · 2019Article
- Computational Approaches to Design and Test Plant Synthetic Metabolic Pathways.Plant physiology · 2019Review
- RetroRules: a database of reaction rules for engineering biology.Nucleic acids research · 2019Article
- Pathway design using de novo steps through uncharted biochemical spaces.Nature communications · 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
- Predicting novel substrates for enzymes with minimal experimental effort with active learning.Metabolic engineering · 2017Article
- A review of parameters and heuristics for guiding metabolic pathfinding.Journal of cheminformatics · 2017Review
- Engineering biological systems using automated biofoundries.Metabolic engineering · 2017Review
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Authors and funding
5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
As metabolic engineering and synthetic biology progress toward reaching the goal of a more sustainable use of biological resources, the need of increasing the number of value-added chemicals that can be produced in industrial organisms becomes more imperative. Exploring, however, the vast possibility of pathways amenable to engineering through heterologous genes expression in a chassis organism is complex and unattainable manually. Here, we present XTMS, a web-based pathway analysis platform available at http://xtms.issb.genopole.fr, which provides full access to the set of pathways that can be imported into a chassis organism such as Escherichia coli through the application of an Extended Metabolic Space modeling framework. The XTMS approach consists on determining the set of biochemical transformations that can potentially be processed in vivo as modeled by molecular signatures, a specific coding system for derivation of reaction rules for metabolic reactions and enumeration of all the corresponding substrates and products. Most promising routes are described in terms of metabolite exchange, maximum allowable pathway yield, toxicity and enzyme efficiency. By answering such critical design points, XTMS not only paves the road toward the rationalization of metabolic engineering, but also opens new processing possibilities for non-natural metabolites and novel enzymatic transformations.
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