A small molecule often has several different binding poses in the binding site of a target. We performed the free energy calculations for the system including such features by the alchemical transformation combined with metadynamics. The restraining harmonic potentials (one distance, two angles and three dihedrals) were used to keep connection with standard state condition during the ligand decoupling process. Binding free energies were evaluated using the multistate Bennett’s acceptance ratio method (MBAR) with stochastic dynamics to sample the potential energy differences between different intermediate states. Computed free energies were in good agreement with the experimental value.<br/>

Binding free energy study of a small molecule to a target by metadynamics and alchemical transformation

251st National Meeting (2016)

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