Table 3.

Comparative Performance of MutaBind2 and Three Methods for Predicting Mutations Highly Decreasing and Increasing Binding Affinity on the Independent Test Set of S1748

	MutaBind2	MutaBind	BeAtMuSiC	FoldX
Highly decreasing
Sensitivity	0.75	0.86	0.73	0.58
Specificity	0.89	0.82	0.87	0.94
MCC	0.63	0.63	0.58	0.57
AUC	0.82	0.82	0.79	0.79
Highly increasing
Sensitivity	0.55	0	0	0.44
Specificity	0.99	1.00	1.00	0.99
MCC	0.64	−0.01	0	0.51
AUC	0.86	0.65∗	0.56∗	0.74∗

MutaBind2 was retrained on the dataset “Skempi + Reverse.”

MCC, Matthews correlation coefficient.

∗p value < 0.01 calculated by Delong test (DeLong et al., 1988) comparing AUC (area under the ROC curve) produced by a given method and AUC produced by MutaBind2; points to significant differences in performance. See also Figure S6.