Figure 1: For me there is no intrinsic difference between the free energy calculations shown in panel D and F, both transformations should be performed in the bound and unbound states to obtain meaningful results, and both should be termed relative calculations (ΔΔG). Maybe it could be more clearly indicated in general if a whole molecule is decoupled and if only a part of a molecule is transformed?
Figure 1: For me there is no intrinsic difference between the free energy calculations shown in panel D and F, both transformations should be performed in the bound and unbound states to obtain meaningful results, and both should be termed relative calculations (ΔΔG). Maybe it could be more clearly indicated in general if a whole molecule is decoupled and if only a part of a molecule is transformed?