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• W2024226970 endingPage "13417" @default.
• W2024226970 startingPage "13411" @default.
• W2024226970 abstract "A comparative analysis is provided of the effect of different solvent models on the calculation of a potential of mean force (PMF) for determining the absolute binding affinity of the small molecule inhibitor pteroic acid bound to ricin toxin A-chain (RTA). Solvent models include the distance-dependent dielectric constant, several different generalized Born (GB) approximations, and a hybrid explicit/GB-based implicit solvent model. We found that the simpler approximation of dielectric screening and a GB model, with Born radii fitted to a switching-window dielectric-boundary surface Poisson solvent model, severely overpredicted the binding affinity as compared to the experimental value, estimated to range from −4.4 to −6.0 kcal/mol. In contrast, GB models that are parametrized to fit the Lee-Richards molecular surface performed much better, predicting binding free energy within 1−3 kcal/mol of experimental estimates. However, the predicted free-energy profiles of these GB models displayed alternative binding modes not observed in the crystal structure. Finally, the most rigorous and computationally costly approach in this work, which used a hybrid explicit/implicit solvent model, correctly determined a binding funnel in the PMF near the crystallographic bound state and predicted an absolute binding affinity that was 2 kcal/mol more favorable than the estimated experimental binding affinity." @default.
• W2024226970 created "2016-06-24" @default.
• W2024226970 creator A5050156659 @default.
• W2024226970 creator A5088195904 @default.
• W2024226970 date "2008-09-27" @default.
• W2024226970 modified "2023-10-18" @default.
• W2024226970 title "Calculation of Absolute Ligand Binding Free Energy to a Ribosome-Targeting Protein as a Function of Solvent Model" @default.
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• W2024226970 doi "https://doi.org/10.1021/jp802460p" @default.
• W2024226970 hasPubMedId "https://pubmed.ncbi.nlm.nih.gov/18821791" @default.
• W2024226970 hasPublicationYear "2008" @default.
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