ReviewFrontiers in molecular biosciences2019
Modeling Crowded Environment in Molecular Simulations.
Review in Frontiers in molecular biosciences, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 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.
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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
21 citing papers in PubMed.
- Crowder-specific modulation of hepatitis C virus NS3/4A protease activity and local structural dynamics.Protein science : a publication of the Protein Society · 2026Article
- Article
- PEG-mCherry interactions beyond classical macromolecular crowding.Protein science : a publication of the Protein Society · 2025Article
- Molecular Crowding by Computational Approaches.Sub-cellular biochemistry · 2025Review
- Simulations of pH and thermal effects on SARS-CoV-2 spike glycoprotein.Frontiers in molecular biosciences · 2025Article
- 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
- Viscosity Prediction of High-Concentration Antibody Solutions with Atomistic Simulations.Journal of chemical information and modeling · 2023Article
- Fibrillization Process of Human Amyloid-Beta Protein (1-40) under a Molecular Crowding Environment Mimicking the Interior of Living Cells Using Cell Debris.Molecules (Basel, Switzerland) · 2023Article
- Effects of Homogeneous and Heterogeneous Crowding on Translational Diffusion of Rigid Bovine Serum Albumin and Disordered Alfa-Casein.International journal of molecular sciences · 2023Article
- Conformational ensembles explain NMR spectra of frozen intrinsically disordered proteins.Protein science : a publication of the Protein Society · 2023Article
- Varying molecular interactions explain aspects of crowder-dependent enzyme function of a viral protease.PLoS computational biology · 2023Article
- Monitoring In Vitro Extracellular Matrix Protein Conformations in the Presence of Biomimetic Bone-Regeneration Scaffolds Using Functionalized Gold-Edge-Coated Triangular Silver Nanoparticles.Nanomaterials (Basel, Switzerland) · 2022Article
- Review
- J-aggregation of 5, 10, 15, 20-tetraphenyl-21H, 23H-porphinetetrasulfonic acid in a molecular crowding environment simulated using dextran.Analytical sciences : the international journal of the Japan Society for Analytical Chemistry · 2022Article
- Short-Time Transport Properties of Bidisperse Suspensions of Immunoglobulins and Serum Albumins Consistent with a Colloid Physics Picture.The journal of physical chemistry. B · 2022Article
- Atomistic Simulation of Lysozyme in Solutions Crowded by Tetraethylene Glycol: Force Field Dependence.Molecules (Basel, Switzerland) · 2022Article
- Improving coarse-grained models of protein folding through weighting of polar-polar/hydrophobic-hydrophobic interactions into crowded spaces.Journal of molecular modeling · 2022Article
- Observed steric crowding at modest coverage requires a particular membrane-binding scheme or a complementary mechanism.Biophysical journal · 2022Article
- Modeling of the thermal properties of SARS-CoV-2 S-protein.Frontiers in molecular biosciences · 2022Article
Corrections and comments
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Authors and funding
3 authors.
Funding
Abstract
Biomolecules perform their various functions in living cells, namely in an environment that is crowded by many macromolecules. Thus, simulating the dynamics and interactions of biomolecules should take into account not only water and ions but also other binding partners, metabolites, lipids and macromolecules found in cells. In the last decade, research on how to model macromolecular crowders around proteins in order to simulate their dynamics in models of cellular environments has gained a lot of attention. In this mini-review we focus on the models of crowding agents that have been used in computer modeling studies of proteins and peptides, especially via molecular dynamics simulations.
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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.