ArticleJournal of molecular biology2022
Building Structural Models of a Whole Mycoplasma Cell.
Article in Journal of molecular biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
What it found
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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.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
44 citing papers in PubMed, 73 citations in OpenAlex.
- Process bigraphs and the architecture of compositional systems biology.PLoS computational biology · 2026Article
- Cryo-electron tomography of Nipah virus structural protein complexes in virus-like particles.bioRxiv : the preprint server for biology · 2026Article
- Simulation of cell-size systems at long timescales with flexible protein structures.bioRxiv : the preprint server for biology · 2026Article
- Cellular and molecular representations: Following the lesson of David Goodsell.Protein science : a publication of the Protein Society · 2026Article
- Molecular architecture of Influenza A virions.bioRxiv : the preprint server for biology · 2026Article
- Compartment-guided assembly of large-scale molecular models with Bentopy.Protein science : a publication of the Protein Society · 2026Article
- Artificial intelligence-enabled multi-scale virtual cell: perspective, challenges, and opportunities.Briefings in bioinformatics · 2026Review
- QSProteome: a community-driven interactive platform for large-scale exploration and evaluation of predicted protein complex structures.Nucleic acids research · 2026Article
- Coupling Molecular and Cellular Dynamics in a Large-Scale Monte Carlo Simulation.International journal of molecular sciences · 2025Article
- Start early and pack light: Collaborative adventures in theory and experiment.Seminars in cell & developmental biology · 2025Review
- Molecular dynamics simulations of biological membranes and membrane-associated phenomena across scales.Current opinion in structural biology · 2025Review
- Build the virtual cell with artificial intelligence: a perspective for cancer research.Military Medical Research · 2025Article
- Recent Progress in Modeling and Simulation of Biomolecular Crowding and Condensation Inside Cells.Journal of chemical information and modeling · 2024Review
- How to build the virtual cell with artificial intelligence: Priorities and opportunities.Cell · 2024Article
- Foundations of a Compositional Systems Biology.ArXiv · 2024Article
- How to Build the Virtual Cell with Artificial Intelligence: Priorities and Opportunities.ArXiv · 2024Article
- Mesoscale explorer: Visual exploration of large-scale molecular models.Protein science : a publication of the Protein Society · 2024Article
- Mesoscale Explorer - Visual Exploration of Large-Scale Molecular Models.bioRxiv : the preprint server for biology · 2024Article
- Multifaceted Activity of Fabimycin: Insights from Molecular Dynamics Studies on Bacterial Membrane Models.Journal of chemical information and modeling · 2024Article
- Replicating Chromosomes in Whole-Cell Models of Bacteria.Methods in molecular biology (Clifton, N.J.) · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 3 institutions in 1 country.
Funding
Abstract
Building structural models of entire cells has been a long-standing cross-discipline challenge for the research community, as it requires an unprecedented level of integration between multiple sources of biological data and enhanced methods for computational modeling and visualization. Here, we present the first 3D structural models of an entire Mycoplasma genitalium (MG) cell, built using the CellPACK suite of computational modeling tools. Our model recapitulates the data described in recent whole-cell system biology simulations and provides a structural representation for all MG proteins, DNA and RNA molecules, obtained by combining experimental and homology-modeled structures and lattice-based models of the genome. We establish a framework for gathering, curating and evaluating these structures, exposing current weaknesses of modeling methods and the boundaries of MG structural knowledge, and visualization methods to explore functional characteristics of the genome and proteome. We compare two approaches for data gathering, a manually-curated workflow and an automated workflow that uses homologous structures, both of which are appropriate for the analysis of mesoscale properties such as crowding and volume occupancy. Analysis of model quality provides estimates of the regularization that will be required when these models are used as starting points for atomic molecular dynamics simulations.
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What OpenQuestion holds
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.