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- W2897679964 endingPage "6049" @default.
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- W2897679964 abstract "We introduce a number of computationally inexpensive modifications to the MM/PBSA and MM/GBSA estimators for binding free energies, which are based on average receptor–ligand interaction energies in simulations of a noncovalent complex, to improve the treatment of entropy: second- and higher-order terms in a cumulant expansion and a confining potential on ligand external degrees of freedom. We also consider a filter for snapshots where ligands have drifted from the initial binding pose. The variations were tested on six sets of systems for which binding modes and free energies have previously been experimentally determined. For some data sets, none of the tested estimators led to results significantly correlated with measured free energies. In data sets with nontrivial correlation, a ligand RMSD cutoff of 3 Å and a second-order truncation of the cumulant expansion was found to be comparable or better than the average interaction energy by several statistical metrics." @default.
- W2897679964 created "2018-10-26" @default.
- W2897679964 creator A5032415345 @default.
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- W2897679964 creator A5045836144 @default.
- W2897679964 creator A5074501688 @default.
- W2897679964 creator A5087396555 @default.
- W2897679964 date "2018-10-08" @default.
- W2897679964 modified "2023-10-16" @default.
- W2897679964 title "Simple Entropy Terms for End-Point Binding Free Energy Calculations" @default.
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- W2897679964 doi "https://doi.org/10.1021/acs.jctc.8b00418" @default.
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- W2897679964 hasPublicationYear "2018" @default.
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