ReviewJournal of molecular biology2016
Challenges in structural approaches to cell modeling.
Review in Journal of molecular biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 33 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
33 citing papers in PubMed.
- Simulation of cell-size systems at long timescales with flexible protein structures.bioRxiv : the preprint server for biology · 2026Article
- Article
- GRAMMCell: Docking-based Cell Modeling Resource.Journal of molecular biology · 2025Article
- Efficient Design of AffilinInternational journal of molecular sciences · 2025Article
- Highly Optimized Simulation of Atomic Resolution Cell-Like Protein Environment.The journal of physical chemistry. B · 2025Article
- Diffusion of proteins in crowded solutions studied by docking-based modeling.The Journal of chemical physics · 2024Article
- 3D models of fungal chromosomes to enhance visual integration of omics data.NAR genomics and bioinformatics · 2023Article
- Mesoscience in cell biology and cancer research.Cancer innovation · 2022Review
- Docking-based long timescale simulation of cell-size protein systems at atomic resolution.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- Building Structural Models of a Whole Mycoplasma Cell.Journal of molecular biology · 2022Article
- Integrative structural modelling and visualisation of a cellular organelle.QRB discovery · 2022Article
- Size of the protein-protein energy funnel in crowded environment.Frontiers in molecular biosciences · 2022Article
- Understanding the Targeting Mechanisms of Multi-Specific Biologics in Immunotherapy with Multiscale Modeling.iScience · 2020Article
- Challenges in protein docking.Current opinion in structural biology · 2020Review
- Application of docking methodologies to modeled proteins.Proteins · 2020Article
- Art and Science of the Cellular Mesoscale.Trends in biochemical sciences · 2020Review
- Whole-Cell Models and Simulations in Molecular Detail.Annual review of cell and developmental biology · 2019Review
- Computational approaches to macromolecular interactions in the cell.Current opinion in structural biology · 2019Review
- Modeling Crowded Environment in Molecular Simulations.Frontiers in molecular biosciences · 2019Review
- Perspectives on Structural Molecular Biology Visualization: From Past to Present.Journal of molecular biology · 2018Review
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.
Funding
Abstract
Computational modeling is essential for structural characterization of biomolecular mechanisms across the broad spectrum of scales. Adequate understanding of biomolecular mechanisms inherently involves our ability to model them. Structural modeling of individual biomolecules and their interactions has been rapidly progressing. However, in terms of the broader picture, the focus is shifting toward larger systems, up to the level of a cell. Such modeling involves a more dynamic and realistic representation of the interactomes in vivo, in a crowded cellular environment, as well as membranes and membrane proteins, and other cellular components. Structural modeling of a cell complements computational approaches to cellular mechanisms based on differential equations, graph models, and other techniques to model biological networks, imaging data, etc. Structural modeling along with other computational and experimental approaches will provide a fundamental understanding of life at the molecular level and lead to important applications to biology and medicine. A cross section of diverse approaches presented in this review illustrates the developing shift from the structural modeling of individual molecules to that of cell biology. Studies in several related areas are covered: biological networks; automated construction of three-dimensional cell models using experimental data; modeling of protein complexes; prediction of non-specific and transient protein interactions; thermodynamic and kinetic effects of crowding; cellular membrane modeling; and modeling of chromosomes. The review presents an expert opinion on the current state-of-the-art in these various aspects of structural modeling in cellular biology, and the prospects of future developments in this emerging field.
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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.