Improving Prediction Accuracy of Binding Free Energies and Poses of HIV Integrase Complexes Using the Binding Energy Distribution Analysis Method with Flattening Potentials.

Abstract excerpt

To accelerate conformation sampling of slow dynamics from receptor or ligand, we introduced flattening potentials on selected bonded and nonbonded intramolecular interactions to the binding energy distribution analysis method (BEDAM) for calculating absolute binding free energies of protein-ligand complexes using an implicit solvent model and implemented flattening BEDAM using the asynchronous replica exchange...

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