ArticleEuropean biophysics journal : EBJ2012
Solvating atomic level fine-grained proteins in supra-molecular level coarse-grained water for molecular dynamics simulations.
Article in European biophysics journal : EBJ, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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10 citing papers in PubMed, 48 citations in OpenAlex.
- Multiscale Neural Network Potential with Anisotropic Message Passing for the Fast and Accurate Simulation of Protein Dynamics and Enzymatic Reactions.Journal of the American Chemical Society · 2026Article
- Simulations of Functional Motions of Super Large Biomolecules with a Mixed-Resolution Model.Journal of chemical theory and computation · 2024Article
- Research and study of 2-((4,6 dimethyl pyrimidine-2-yle) thio)-N-phenyl acetamide derivatives as inhibitors of sirtuin 2 protein for the treatment of cancer using QSAR, molecular docking and molecular dynamic simulation.Journal of molecular modeling · 2022Article
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- Molecular simulations of self-assembling bio-inspired supramolecular systems and their connection to experiments.Chemical Society reviews · 2018Review
- Adaptive resolution simulations of biomolecular systems.European biophysics journal : EBJ · 2017Review
- A New Mixed All-Atom/Coarse-Grained Model: Application to Melittin Aggregation in Aqueous Solution.Journal of chemical theory and computation · 2017Article
- Hydration Properties and Solvent Effects for All-Atom Solutes in Polarizable Coarse-Grained Water.The journal of physical chemistry. B · 2016Article
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Authors and funding
3 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Simulation of the dynamics of a protein in aqueous solution using an atomic model for both the protein and the many water molecules is still computationally extremely demanding considering the time scale of protein motions. The use of supra-atomic or supra-molecular coarse-grained (CG) models may enhance the computational efficiency, but inevitably at the cost of reduced accuracy. Coarse-graining solvent degrees of freedom is likely to yield a favourable balance between reduced accuracy and enhanced computational speed. Here, the use of a supra-molecular coarse-grained water model that largely preserves the thermodynamic and dielectric properties of atomic level fine-grained (FG) water in molecular dynamics simulations of an atomic model for four proteins is investigated. The results of using an FG, a CG, an implicit, or a vacuum solvent environment of the four proteins are compared, and for hen egg-white lysozyme a comparison to NMR data is made. The mixed-grained simulations do not show large differences compared to the FG atomic level simulations, apart from an increased tendency to form hydrogen bonds between long side chains, which is due to the reduced ability of the supra-molecular CG beads that represent five FG water molecules to make solvent-protein hydrogen bonds. But, the mixed-grained simulations are at least an order of magnitude faster than the atomic level ones.
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