Fig. 1: A thermodynamic cycle for computing relative binding free energies.
From: Fast free energy estimates from λ-dynamics with bias-updated Gibbs sampling
Two ligands (L1 and L2) with different substituents (represented as a methyl group in blue or an iso-propyl group in red) are represented as bound to a protein (in gray) or unbound in solution. Relative binding free energies between L1 and L2 can be computed by alchemically transforming L1 into L2 in bound and unbound states.
