Fig. 3: Estimating binding pocket volume and its contribution to absolute binding free energy.
From: Binding affinity estimation from restrained umbrella sampling simulations
a, Grid PMF (ΔG(x)) associated with grid points with the 20-lowest PMF values (black) along with estimated ΔGP based on these grid points (shown in an accumulative manner in magenta). The distance-based BEUS simulations with no restraints are used for these calculations. The dashed line shows the estimated ΔGP based on all visited grid points inside or outside the binding pocket. The x axis shows the ranking of these 20 grid points from lowest PMF onwards. b, Binding pocket volume (VP) calculated from the 20-lowest grid PMF values (similar to a). The dashed line shows the VP estimated from all visited grid points inside or outside the binding pocket. See ‘Theoretical foundation’ in Methods for more details.
