Table 6.

Analysis of Binding Affinity Prediction Methods.

	Number of Methods Predicted as Affinity Reducing
Prediction	All 3	Only 2	Only 1	Majority	Minority	None
Affinity Reducing	108	102	97	210	179	82
Tolerated	27	63	147	90	528	381
Fraction Correct	0.80	0.62	0.40	0.70	0.75	0.82
Fraction Affinity Reducing	0.28	0.26	0.25	0.54	0.46	0.21
Fraction Tolerated	0.04	0.10	0.24	0.15	0.85	0.62
	Discovery Studio		Prime		MacroModel
Prediction	AR	Tol	AR	Tol	AR	Tol
Affinity Reducing	243	146	189	200	193	196
Tolerated	135	483	131	487	88	530
Fraction Correct	0.64	0.77	0.59	0.71	0.69	0.73
Fraction Affinity Reducing	0.62	0.38	0.49	0.51	0.50	0.50
Fraction Tolerated	0.22	0.78	0.21	0.79	0.14	0.86

The total number of affinity reducing and tolerated mutants found in each prediction group is shown for: (top) number of methods predicting a mutant to be affinity reducing, and (bottom) individual methods predictions of affinity reducing (AR) and tolerated (Tol) mutations. The Fraction correct is the true positive rate for “All 3” AR (n=3), “Only 2” AR (n=2), “Only 1” AR (n=1) and “Majority” AR (n>=2) predictions and “AR” predictions for individual methods, and the true negative rate for “Minority” AR (n<=1) and “None” AR n=0 predictions and “Tol” predictions for individual methods. The fraction affinity reducing and fraction tolerated are number of experimentally determined affinity reducing and tolerated mutants in that group divided by the total number of affinity reducing or tolerated mutants, respectively.