ArticleBMC systems biology2016
Systems biology of the structural proteome.
Article in BMC systems biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 32 papers.
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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.
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Who cites it
32 citing papers in PubMed.
- Toward a systems metabolic engineering approach to improve thermotolerance of Escherichia coli.Microbial cell factories · 2026Review
- Metabolic Objectives and Trade-Offs: Inference and Applications.Metabolites · 2025Review
- Genome-scale metabolic models consistently predictFrontiers in bioinformatics · 2023Article
- Construction of Multiscale Genome-Scale Metabolic Models: Frameworks and Challenges.Biomolecules · 2022Review
- ECMpy, a Simplified Workflow for Constructing Enzymatic Constrained Metabolic Network Model.Biomolecules · 2022Article
- Constraint-Based Reconstruction and Analyses of Metabolic Models: Open-Source Python Tools and Applications to Cancer.Frontiers in oncology · 2022Review
- Next-Generation Genome-Scale Metabolic Modeling through Integration of Regulatory Mechanisms.Metabolites · 2021Review
- Integration of enzyme constraints in a genome-scale metabolic model of Aspergillus niger improves phenotype predictions.Microbial cell factories · 2021Article
- Bacterial fitness landscapes stratify based on proteome allocation associated with discrete aero-types.PLoS computational biology · 2021Article
- The Expanding Computational Toolbox for Engineering Microbial Phenotypes at the Genome Scale.Microorganisms · 2020Review
- Reconstructing organisms in silico: genome-scale models and their emerging applications.Nature reviews. Microbiology · 2020Review
- Systems biology analysis of the Clostridioides difficile core-genome contextualizes microenvironmental evolutionary pressures leading to genotypic and phenotypic divergence.NPJ systems biology and applications · 2020Article
- Structural Biology in the Multi-Omics Era.Journal of chemical information and modeling · 2020Article
- Adaptations of Escherichia coli strains to oxidative stress are reflected in properties of their structural proteomes.BMC bioinformatics · 2020Article
- Current status and applications of genome-scale metabolic models.Genome biology · 2019Review
- Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models.Nature communications · 2018Article
- Modeling the multi-scale mechanisms of macromolecular resource allocation.Current opinion in microbiology · 2018Review
- ssbio: a Python framework for structural systems biology.Bioinformatics (Oxford, England) · 2018Article
- Recon3D enables a three-dimensional view of gene variation in human metabolism.Nature biotechnology · 2018Article
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Corrections and comments
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Authors and funding
10 authors.
Funding
Abstract
backgroundThe success of genome-scale models (GEMs) can be attributed to the high-quality, bottom-up reconstructions of metabolic, protein synthesis, and transcriptional regulatory networks on an organism-specific basis. Such reconstructions are biochemically, genetically, and genomically structured knowledge bases that can be converted into a mathematical format to enable a myriad of computational biological studies. In recent years, genome-scale reconstructions have been extended to include protein structural information, which has opened up new vistas in systems biology research and empowered applications in structural systems biology and systems pharmacology.
resultsHere, we present the generation, application, and dissemination of genome-scale models with protein structures (GEM-PRO) for Escherichia coli and Thermotoga maritima. We show the utility of integrating molecular scale analyses with systems biology approaches by discussing several comparative analyses on the temperature dependence of growth, the distribution of protein fold families, substrate specificity, and characteristic features of whole cell proteomes. Finally, to aid in the grand challenge of big data to knowledge, we provide several explicit tutorials of how protein-related information can be linked to genome-scale models in a public GitHub repository ( https://github.com/SBRG/GEMPro/tree/master/GEMPro_recon/).
conclusionsTranslating genome-scale, protein-related information to structured data in the format of a GEM provides a direct mapping of gene to gene-product to protein structure to biochemical reaction to network states to phenotypic function. Integration of molecular-level details of individual proteins, such as their physical, chemical, and structural properties, further expands the description of biochemical network-level properties, and can ultimately influence how to model and predict whole cell phenotypes as well as perform comparative systems biology approaches to study differences between organisms. GEM-PRO offers insight into the physical embodiment of an organism's genotype, and its use in this comparative framework enables exploration of adaptive strategies for these organisms, opening the door to many new lines of research. With these provided tools, tutorials, and background, the reader will be in a position to run GEM-PRO for their own purposes.
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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.