Table 1. Summary of the Evaluation of PPI-Affinity and State-of-the-Art BA Predictors on Two Sets of Protein–Protein Affinity Data^a.

	test set 1		test set 2
method	R	MAE (kcal/mol)	R	MAE (kcal/mol)
PRODIGY	0.74	1.4	0.31	2.5
DFIRE	0.60	4.6	0.10	25.4
CP_PIE	–0.52	8.8	–0.10	11.0
ISLAND	0.38	2.1	0.27	2.2
PPI-Affinity	0.62	1.8	0.50	1.8

^aThe performance is expressed as the Pearson’s correlation coefficient (R) between experimental and predicted BA. The test set 1 corresponds to the benchmark employed by Vangone and Bonvin,²¹ while the test set 2 corresponds to the hold-out set of 90 data points taken from PDBbind (v.2020). The performance for the other methods on test set 1 was reported by Vangone and Bonvin.²¹ The negative values of the correlation coefficients indicate that the corresponding method predicts unbinding free energy.