ArticleJournal of chemical theory and computation2013
An FFT-based method for modeling protein folding and binding under crowding: benchmarking on ellipsoidal and all-atom crowders.
Article in Journal of chemical theory and computation, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 28 papers.
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Who cites it
28 citing papers in PubMed.
- Mesoscale Heterogeneity Shapes Molecular Selectivity and Transport in Biomolecular Condensates.bioRxiv : the preprint server for biology · 2026Article
- Fast calculation of small-angle scattering profiles of dense protein solutions modeled at the all-atom level.Proceedings of the National Academy of Sciences of the United States of America · 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
- Review
- Calculating Structure Factors of Protein Solutions by Atomistic Modeling of Protein-Protein Interactions.Physica A · 2024Article
- Calculating Structure Factors of Protein Solutions by Atomistic Modeling of Protein-Protein Interactions.bioRxiv : the preprint server for biology · 2024Article
- Surface Charge Can Modulate Phase Separation of Multidomain Proteins.Journal of the American Chemical Society · 2024Article
- Atomistic modeling of liquid-liquid phase equilibrium explains dependence of critical temperature on γ-crystallin sequence.Communications biology · 2023Article
- Atomistic Modeling of Liquid-Liquid Phase Equilibrium Explains Dependence of Critical Temperature on γ-Crystallin Sequence.bioRxiv : the preprint server for biology · 2023Article
- 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
- Characterizing protein kinase A (PKA) subunits as macromolecular regulators of PKA RIα liquid-liquid phase separation.The Journal of chemical physics · 2021Article
- Calculation of Second Virial Coefficients of Atomistic Proteins Using Fast Fourier Transform.The journal of physical chemistry. B · 2019Article
- Transfer Free Energies of Test Proteins Into Crowded Protein Solutions Have Simple Dependence on Crowder Concentration.Frontiers in molecular biosciences · 2019Article
- Atomistic Modeling of Intrinsically Disordered Proteins Under Polyethylene Glycol Crowding: Quantitative Comparison with Experimental Data and Implication of Protein-Crowder Attraction.The journal of physical chemistry. B · 2018Article
- Power transformations improve interpolation of grids for molecular mechanics interaction energies.Journal of computational chemistry · 2018Article
- Using the fast fourier transform in binding free energy calculations.Journal of computational chemistry · 2018Article
- Explicit Incorporation of Hard and Soft Protein-Protein Interactions into Models for Crowding Effects in Protein Mixtures. 2. Effects of Varying Hard and Soft Interactions upon Prototypical Chemical Equilibria.The journal of physical chemistry. B · 2017Article
- Protein folding, binding, and droplet formation in cell-like conditions.Current opinion in structural biology · 2017Review
- Thermodynamics of Macromolecular Association in Heterogeneous Crowding Environments: Theoretical and Simulation Studies with a Simplified Model.The journal of physical chemistry. B · 2016Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
It is now well recognized that macromolecular crowding can exert significant effects on protein folding and binding stability. In order to calculate such effects in direct simulations of proteins mixed with bystander macromolecules, the latter (referred to as crowders) are usually modeled as spheres and the proteins represented at a coarse-grained level. Our recently developed postprocessing approach allows the proteins to be represented at the all-atom level but, for computational efficiency, has only been implemented for spherical crowders. Modeling crowder molecules in cellular environments and
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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.