Table 3. Comparing RaSP predictions from crystal and AlphaFold 2 (AF2) structures.

Pearson correlation coefficients ($\rho$) between RaSP $\mathrm{\Delta }\mathrm{\Delta }G$ predictions using either two different crystal structures or a crystal structure and an AlphaFold 2 structure for six test proteins: PRMT5 (X1: 6V0P_A, X2: 4GQB_A), PKM (X1: 6B6U_A, X2: 6NU5_A), FTH1 (X1: 4Y08_A, X2: 4OYN_A), FTL (X1: 5LG8_A, X2: 2FFX_J), PSMA2 (X1: 5LE5_A, X2: 5LE5_O) and GNB1 (X1: 6CRK_B, X2: 5UKL_B). We also divided the analysis into residues with high (pLDDT ≥ 0.9) and medium-low (pLDDT <0.9) pLDDT scores from AlphaFold 2.

Protein	All [$\rho$]			High AF2 pLDDT [$\rho$]			Medium-Low AF2 pLDDT [$\rho$]
	X1-X2	X1-AF2	X2-AF2	X1-X2	X1-AF2	X2-AF2	X1-X2	X1-AF2	X2-AF2
PRMT5	0.93	0.89	0.95	-	0.90	0.95	-	0.66	0.89
PKM	0.99	0.95	0.95	-	0.95	0.95	-	0.88	0.89
FTH1	0.99	0.97	0.97	-	0.97	0.97	-	0.92	0.95
FTL	0.97	0.96	0.97	-	0.96	0.97	-	0.96	0.94
PSMA2	0.99	0.95	0.95	-	0.96	0.96	-	0.78	0.80
GNB1	0.96	0.94	0.94	-	0.94	0.94	-	0.93	0.89