Figure 3. Scatter plot of predicted vs experimental binding affinities.
The predictions were made according to the inter-residue contacts (ICs)/non-interacting surface (NIS)-based model (Model 6, Equation 2) for the cleaned dataset of 81 protein–protein complexes. The correlation for all 81 complexes yields an R of −0.73 (ρ < 0.0001) with a RMSE of 1.89 kcal mol−1. When only rigid cases (interface RMSD between superimposed free and bound components ≤1.0 Å, red triangles) are considered, the correlation increases to R = −0.75 (ρ < 0.0001) with a RMSE of 1.88 kcal mol−1, while for flexible cases (interface RMSD >1.0 Å; yellow rhombus) R = −0.73 (ρ < 0.0001) with a RMSE of 1.88 kcal mol−1. The x = y line is shown as reference; binding affinities are reported as absolute values.