ArticleBiomolecules2022
ECMpy, a Simplified Workflow for Constructing Enzymatic Constrained Metabolic Network Model.
Article in Biomolecules, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed.
- EINN: An enzyme-informed neural network guided by an enzyme-constrained genome-scale metabolic model.Synthetic and systems biotechnology · 2027Article
- Article
- SynBioGPT2: A dynamic reasoning framework enables high-fidelity design of microbial cell factories.Biodesign research · 2026Article
- Enzyme-constrained genome-scale modeling resolves growth-production trade-offs in fermentative biohydrogen production.Environmental science and ecotechnology · 2026Article
- PYF: a multi-functional algorithm for predicting production and optimizing metabolic engineering strategy in Escherichia coli microbial consortia.Briefings in bioinformatics · 2025Article
- Evolution and applications of genome-scale metabolic models in yeast systems biology studies.FEMS yeast research · 2025Review
- Metabolic modeling of host-microbe interactions.Computational and structural biotechnology journal · 2025Review
- Algorithm of spatial-temporal simulation for environment-strain interactions in strain-strain consortia based on resource competition mechanism.Computational and structural biotechnology journal · 2024Article
- ECMpy 2.0: A Python package for automated construction and analysis of enzyme-constrained models.Synthetic and systems biotechnology · 2024Article
- Current State, Challenges, and Opportunities in Genome-Scale Resource Allocation Models: A Mathematical Perspective.Metabolites · 2024Review
- Omics data analysis reveals the system-level constraint on cellular amino acid composition.Synthetic and systems biotechnology · 2024Article
- Construction of an enzyme-constrained metabolic network model for Myceliophthora thermophila using machine learning-based kMicrobial cell factories · 2024Article
- DeepSub: Utilizing Deep Learning for Predicting the Number of Subunits in Homo-Oligomeric Protein Complexes.International journal of molecular sciences · 2024Article
- Reconstruction, simulation and analysis of enzyme-constrained metabolic models using GECKO Toolbox 3.0.Nature protocols · 2024Review
- Co-Cultivated Enzyme Constraint Metabolic Network Model for Rational Guidance in Constructing Synthetic Consortia to Achieve Optimal Pathway Allocation Prediction.Advanced science (Weinheim, Baden-Wurttemberg, Germany) · 2024Article
- Simultaneous application of enzyme and thermodynamic constraints to metabolic models using an updated Python implementation of GECKO.Microbiology spectrum · 2023Article
- Improving pathway prediction accuracy of constraints-based metabolic network models by treating enzymes as microcompartments.Synthetic and systems biotechnology · 2023Article
- ecBSU1: A Genome-Scale Enzyme-Constrained Model ofMicroorganisms · 2023Article
- Enzyme-constrained metabolic model andComputational and structural biotechnology journal · 2023Article
- Construction and Analysis of an Enzyme-Constrained Metabolic Model ofBiomolecules · 2022Article
Corrections and comments
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Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Genome-scale metabolic models (GEMs) have been widely used for the phenotypic prediction of microorganisms. However, the lack of other constraints in the stoichiometric model often leads to a large metabolic solution space being inaccessible. Inspired by previous studies that take an allocation of macromolecule resources into account, we developed a simplified Python-based workflow for constructing enzymatic constrained metabolic network model (ECMpy) and constructed an enzyme-constrained model for
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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.