ReviewBiochemical Society transactions2018
Model-based metabolism design: constraints for kinetic and stoichiometric models.
Review in Biochemical Society transactions, 2018. 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.
- Comparing kinetic versus stoichiometric priorities in hybrid models of CHO metabolism.NPJ systems biology and applications · 2026Article
- Article
- Pichia pastoris growth-coupled heme biosynthesis analysis using metabolic modelling.Scientific reports · 2023Article
- Local flux coordination and global gene expression regulation in metabolic modeling.Nature communications · 2023Article
- Metabolic Modeling ofMetabolites · 2023Article
- Hybrid computational models of multicellular tumour growth considering glucose metabolism.Computational and structural biotechnology journal · 2023Review
- Integrative Gene Expression and Metabolic Analysis ToolBiomolecules · 2022Article
- Kinetic and Stoichiometric Modeling-Based Analysis of Docosahexaenoic Acid (DHA) Production Potential byMarine drugs · 2022Article
- Path to improving the life cycle and quality of genome-scale models of metabolism.Cell systems · 2021Review
- Synthetic biology as driver for the biologization of materials sciences.Materials today. Bio · 2021Review
- An Early Stage Researcher's Primer on Systems Medicine Terminology.Network and systems medicine · 2021Review
- Sustainable metabolic engineering for sustainability optimisation of industrial biotechnology.Computational and structural biotechnology journal · 2021Review
- Article
- Approaches to Computational Strain Design in the Multiomics Era.Frontiers in microbiology · 2019Article
- A Constraint-Based Model Analysis of Enterocyte Mitochondrial Adaptation to Dietary Interventions of Lipid Type and Lipid Load.Frontiers in physiology · 2018Article
Corrections and comments
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Authors and funding
5 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The implementation of model-based designs in metabolic engineering and synthetic biology may fail. One of the reasons for this failure is that only a part of the real-world complexity is included in models. Still, some knowledge can be simplified and taken into account in the form of optimization constraints to improve the feasibility of model-based designs of metabolic pathways in organisms. Some constraints (mass balance, energy balance, and steady-state assumption) serve as a basis for many modelling approaches. There are others (total enzyme activity constraint and homeostatic constraint) proposed decades ago, but which are frequently ignored in design development. Several new approaches of cellular analysis have made possible the application of constraints like cell size, surface, and resource balance. Constraints for kinetic and stoichiometric models are grouped according to their applicability preconditions in (1) general constraints, (2) organism-level constraints, and (3) experiment-level constraints. General constraints are universal and are applicable for any system. Organism-level constraints are applicable for biological systems and usually are organism-specific, but these constraints can be applied without information about experimental conditions. To apply experimental-level constraints, peculiarities of the organism and the experimental set-up have to be taken into account to calculate the values of constraints. The limitations of applicability of particular constraints for kinetic and stoichiometric models are addressed.
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