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Chemistry · L5 · Free-Energy Perturbation Alchemical Pathway

How FEP calculates the relative binding free energy between two closely related ligands by alchemically transforming one into the other in both the bound and unbound thermodynamic states.

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Ligand A bound to proteinLigand B bound to proteinLigand A unbound in solventLigand B unbound in solventRelative binding free energy: Delta Delta G equals Delta G bound minus Delta G unboundCompare to experimental relative affinity, refine ligand seriesAlchemical transformation via intermediate lambda stepsAlchemical transformation via intermediate lambda stepsDelta G bound A to BDelta G unbound A to B

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