ArticleThe journal of physical chemistry. B2018
Lattice Models of Bacterial Nucleoids.
Article in The journal of physical chemistry. B, 2018. 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.
- Physical models of bacterial chromosomes.Molecular microbiology · 2025Review
- Replicating Chromosomes in Whole-Cell Models of Bacteria.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Integrative modeling of JCVI-Syn3A nucleoids with a modular approach.Current research in structural biology · 2024Article
- Dynamics of chromosome organization in a minimal bacterial cell.Frontiers in cell and developmental biology · 2023Article
- DNA supercoiling in bacteria: state of play and challenges from a viewpoint of physics based modeling.Frontiers in microbiology · 2023Review
- Mesoscience in cell biology and cancer research.Cancer innovation · 2022Review
- Integrative illustration of a JCVI-syn3A minimal cell.Journal of integrative bioinformatics · 2022Article
- Building Structural Models of a Whole Mycoplasma Cell.Journal of molecular biology · 2022Article
- Direct visualization of the effect of DNA structure and ionic conditions on HU-DNA interactions.Scientific reports · 2021Article
- Moltemplate: A Tool for Coarse-Grained Modeling of Complex Biological Matter and Soft Condensed Matter Physics.Journal of molecular biology · 2021Article
- A Hi-C data-integrated model elucidates E. coli chromosome's multiscale organization at various replication stages.Nucleic acids research · 2021Article
- Generating Chromosome Geometries in a Minimal Cell From Cryo-Electron Tomograms and Chromosome Conformation Capture Maps.Frontiers in molecular biosciences · 2021Article
- Challenges in protein docking.Current opinion in structural biology · 2020Review
- Art and Science of the Cellular Mesoscale.Trends in biochemical sciences · 2020Review
- Mesoscope: A Web-based Tool for Mesoscale Data Integration and Curation.MolVa : Workshop on Molecular Graphics and Visual Analysis of Molecular Data 2020 · 2020Article
- EVR: reconstruction of bacterial chromosome 3D structure models using error-vector resultant algorithm.BMC genomics · 2019Article
- Whole-Cell Models and Simulations in Molecular Detail.Annual review of cell and developmental biology · 2019Review
- Integrative modeling of the HIV-1 ribonucleoprotein complex.PLoS computational biology · 2019Article
- Computational approaches to macromolecular interactions in the cell.Current opinion in structural biology · 2019Review
- Integrative Modeling and Visualization of Exosomes.The Journal of biocommunication · 2019Article
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Authors and funding
3 authors.
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Abstract
Mesoscale molecular modeling is providing a new window into the inner workings of living cells. Modeling of genomes, however, remains a technical challenge, due to their large size and complexity. We describe a lattice method for rapid generation of bacterial nucleoid models that integrates experimental data from a variety of biophysical techniques and provides a starting point for simulation and hypothesis generation. The current method builds models of a circular bacterial genome with supercoiled plectonemes, packed within the small space of the bacterial cell. Lattice models are generated for Mycoplasma genitalium and Escherichia coli nucleoids, and used to simulate interaction data. The method is rapid enough to allow generation of multiple models when analyzing structure/function relationships, and we demonstrate use of the lattice models in creation of an all-atom representation of an entire cell.
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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.