Table VI.

The performance of PSSM and surface area terms using kernel density classification functions

	Features	TPR	TNR	PPV	NPV	ACC	BACC
Surface area from highest resolution biological assembly	Global cutoff for BA surface area	73.0	62.2	78.9	54.2	69.3	67.6
	Global cutoff for monomer surface area	62.7	67.0	78.7	48.1	64.2	64.9
	Wildtype-specific cutoffs for BA	74.2	63.6	79.8	55.9	70.6	68.9
	Wildtype-specific cutoffs for Monomer	62.9	69.0	79.8	48.9	65.0	66.0
Surface area from multiple biological assemblies	Single BA surface area	72.3	65.4	79.5	55.9	69.9	68.8
	Single monomer surface area	66.4	67.8	79.3	52.1	66.9	67.1
	Minimal BA surface area	75.9	63.5	79.4	58.7	71.6	69.7
	Minimal monomer surface area	66.8	67.1	79.0	52.1	66.9	67.0
	Maximal BA surface area	67.4	67.6	79.4	52.8	67.5	67.5
	Maximal monomer surface area	64.6	67.4	78.6	50.7	65.6	66.0
	Averaged BA surface area	74.5	64.6	79.6	57.7	71.0	69.5
	Averaged monomer surface area	67.7	67.1	79.3	52.8	67.5	67.4
Surface area from homo and hetero biological assemblies	Surface area in homo BA	78.2	61.5	80.0	59.0	72.6	69.9
	Surface area in homo monomer	72.4	64.0	79.8	54.2	69.6	68.2
	Surface area in hetero BA	77.2	61.0	79.5	57.6	71.7	69.1
	Surface area in hetero monomer	72.0	63.3	79.4	53.5	69.1	67.6
PSSM scores	Wildtype residue PSSM score	70.7	71.4	67.4	74.5	71.1	71.1
	Mutant residue PSSM score	66.8	79.6	73.3	74.2	73.8	73.2
	dPSSM (Wildtype – mutant PSSM)	76.0	79.0	75.2	79.8	77.7	77.5
	Best of six kernel probabilities	70.4	84.4	79.0	77.3	78.0	77.4
dPSSM from data set balanced for each wildtype amino acid type	Global dPSSM cutoff	73.4	75.5	75.0	73.9	-	74.4
	Wildtype-specific dPSSM cutoffs	73.4	79.3	78.0	74.9	-	76.3
dPSSM from data set balanced for each mutant amino acid type	Global dPSSM cutoff	74.5	77.4	76.7	75.2	-	75.9
	Mutant-specific dPSSM cutoffs	72.8	80.8	79.1	74.8	-	76.8

“BA” = biological assembly

The best method in each section for each accuracy measure is shown in bold italic type.