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• W4379376242 abstract "A novel method combining the maximum entropy principle, the Bayesian-inference of ensembles approach, and the optimization of empirical forward models is presented. Here, we focus on the Karplus parameters for RNA systems, which relate the dihedral angles of γ, β, and the dihedrals in the sugar ring to the corresponding 3J-coupling signal between coupling protons. Extensive molecular simulations are performed on a set of RNA tetramers and hexamers and combined with available nucleic-magnetic-resonance data. Within the new framework, the sampled structural dynamics can be reweighted to match experimental data while the error arising from inaccuracies in the forward models can be corrected simultaneously and consequently does not leak into the reweighted ensemble. Carefully crafted cross-validation procedure and regularization terms enable obtaining transferable Karplus parameters. Our approach identifies the optimal regularization strength and new sets of Karplus parameters balancing good agreement between simulations and experiments with minimal changes to the original ensemble." @default.
• W4379376242 created "2023-06-06" @default.
• W4379376242 creator A5005340330 @default.
• W4379376242 creator A5082187932 @default.
• W4379376242 creator A5084113335 @default.
• W4379376242 date "2023-06-05" @default.
• W4379376242 modified "2023-10-18" @default.
• W4379376242 title "Simultaneous refinement of molecular dynamics ensembles and forward models using experimental data" @default.
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• W4379376242 doi "https://doi.org/10.1063/5.0151163" @default.
• W4379376242 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/37272569" @default.
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