ArticleProceedings of the National Academy of Sciences of the United States of America2022
Docking-based long timescale simulation of cell-size protein systems at atomic resolution.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- From Intermolecular Poses to Thermodynamics Using Subdivided Spheres.The journal of physical chemistry. B · 2026Article
- Simulation of cell-size systems at long timescales with flexible protein structures.bioRxiv : the preprint server for biology · 2026Article
- SimHS-AFMfit-MD: An Integrative Approach for Inferring Alpha-Actinin Atomic Conformational Dynamics.Nano letters · 2026Article
- 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
- Should Artificial Intelligence Play a Durable Role in Biomedical Research and Practice?International journal of molecular sciences · 2024Review
- 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
- Computational Approaches to Predict Protein-Protein Interactions in Crowded Cellular Environments.Chemical reviews · 2024Review
- Assembly of Protein Complexes in and on the Membrane with Predicted Spatial Arrangement Constraints.Journal of molecular biology · 2024Article
- GRAMM Web Server for Protein Docking.Methods in molecular biology (Clifton, N.J.) · 2024Article
- Single-molecule tracking to determine the abundances and stoichiometries of freely-diffusing protein complexes in living cells: Past applications and future prospects.The Journal of chemical physics · 2023Review
- Understanding How Cells Probe the World: A Preliminary Step towards Modeling Cell Behavior?International journal of molecular sciences · 2023Article
- Size of the protein-protein energy funnel in crowded environment.Frontiers in molecular biosciences · 2022Article
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Authors and funding
5 authors.
Funding
Abstract
Computational methodologies are increasingly addressing modeling of the whole cell at the molecular level. Proteins and their interactions are the key component of cellular processes. Techniques for modeling protein interactions, thus far, have included protein docking and molecular simulation. The latter approaches account for the dynamics of the interactions but are relatively slow, if carried out at all-atom resolution, or are significantly coarse grained. Protein docking algorithms are far more efficient in sampling spatial coordinates. However, they do not account for the kinetics of the association (i.e., they do not involve the time coordinate). Our proof-of-concept study bridges the two modeling approaches, developing an approach that can reach unprecedented simulation timescales at all-atom resolution. The global intermolecular energy landscape of a large system of proteins was mapped by the pairwise fast Fourier transform docking and sampled in space and time by Monte Carlo simulations. The simulation protocol was parametrized on existing data and validated on a number of observations from experiments and molecular dynamics simulations. The simulation protocol performed consistently across very different systems of proteins at different protein concentrations. It recapitulated data on the previously observed protein diffusion rates and aggregation. The speed of calculation allows reaching second-long trajectories of protein systems that approach the size of the cells, at atomic resolution.
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