ReviewCurrent opinion in structural biology2022
Protein assembly and crowding simulations.
Review in Current opinion in structural biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 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.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
23 citing papers in PubMed.
- Glycopolymers stabilize protein folding and protein-protein interactions via enthalpic interactions.Protein science : a publication of the Protein Society · 2026Article
- Aggregation of Intrinsically Fluorescent Proteins: Combining Coarse-Grained Molecular Dynamics with Alphafold Predictions.ACS omega · 2025Article
- Simulated Solute Tempering 2: An Efficient and Practical Approach to Protein Conformational Sampling and Binding Events.Journal of chemical theory and computation · 2025Article
- A coarse-grained model for disordered proteins under crowded conditions.Protein science : a publication of the Protein Society · 2025Article
- GRAMMCell: Docking-based Cell Modeling Resource.Journal of molecular biology · 2025Article
- Highly Optimized Simulation of Atomic Resolution Cell-Like Protein Environment.The journal of physical chemistry. B · 2025Article
- PEG-mCherry interactions beyond classical macromolecular crowding.Protein science : a publication of the Protein Society · 2025Article
- A high-throughput platform for single-molecule tracking identifies drug interaction and cellular mechanisms.eLife · 2025Article
- Molecular Crowding by Computational Approaches.Sub-cellular biochemistry · 2025Review
- Liquid-Liquid Phase Separation Associated with Intrinsically Disordered Proteins: Experimental and Computational Tools.Current protein & peptide science · 2025Review
- Clustering of RNA Polymerase II C-Terminal Domain Models upon Phosphorylation.The journal of physical chemistry. B · 2024Article
- Diffusion of proteins in crowded solutions studied by docking-based modeling.The Journal of chemical physics · 2024Article
- Modeling reveals the strength of weak interactions in stacked-ring assembly.Biophysical journal · 2024Article
- Size Sensitivity of Metabolite Diffusion in Macromolecular Crowds.Nano letters · 2024Article
- Computational Approaches to Predict Protein-Protein Interactions in Crowded Cellular Environments.Chemical reviews · 2024Review
- Molecular Crowding: The History and Development of a Scientific Paradigm.Chemical reviews · 2024Review
- Biomolecular dynamics in the 21st century.Biochimica et biophysica acta. General subjects · 2024Review
- Scrutinizing the protein hydration shell from molecular dynamics simulations against consensus small-angle scattering data.Communications chemistry · 2023Article
- Effects of Molecular Crowding on the Structure, Stability, and Interaction with Ligands of G-quadruplexes.ACS omega · 2023Review
- Dynamics of chromosome organization in a minimal bacterial cell.Frontiers in cell and developmental biology · 2023Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
3 authors.
Funding
Abstract
Proteins encounter frequent molecular interactions in biological environments. Computer simulations have become an increasingly important tool in providing mechanistic insights into how such interactions in vivo relate to their biological function. The review here focuses on simulations describing protein assembly and molecular crowding effects as two important aspects that are distinguished mainly by how specific and long-lived protein contacts are. On the topic of crowding, recent simulations have provided new insights into how crowding affects protein folding and stability, modulates enzyme activity, and affects diffusive properties. Recent studies of assembly processes focus on assembly pathways, especially for virus capsids, amyloid aggregation pathways, and the role of multivalent interactions leading to phase separation. Also, discussed are technical challenges in achieving increasingly realistic simulations of interactions in cellular environments.
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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.