Table III.

Interface Residue Prediction Performance of PS-HomPPI on the BM3 Dataset with Three Different Prediction Confidence Zones on Three Levels of Conformational Changes upon Binding

Confidence zones	Conformational change upon binding	Number of predictions (out of 372)	CC	F1	Specificity	Sensitivity
Safe	Rigid	138	0.63	0.64	0.71	0.65
	Medium	22	0.59	0.59	0.72	0.59
	Difficulty	26	0.56	0.55	0.74	0.55
Twilight	Rigid	34	0.46	0.52	0.55	0.59
	Medium	4	0.38	0.4	0.43	0.38
	Difficulty	4	0.54	0.6	0.58	0.63
Dark	Rigid	4	0.12	0.19	0.19	0.38
	Medium	0	–	–	–	–
	Difficulty	0	–	–	–	–
Average		232/372 = 62%	0.58	0.59	0.67	0.61

Only the interfaces between the receptors and ligands are predicted and used by DockRank in ranking docked models. During the evaluation, we consider each partner-specific-predicted receptor–ligand interface as one prediction. For example, for a complex AB:C with two receptor chains A and B and one ligand chain C, we consider four predictions: A|A:B, A|A:C, B|B:A, C|C:A, where A|A:B means the interface of A that interacts with its binding partner B. Sometimes, part of a protein may not have interface predictions from PS-HomPPI because of the lack of aligned residues from putative sequence homologs. These residues are not considered in the evaluation here, because they are not used by DockRank in ranking docked models. Correlation coefficient (CC), F1, specificity, and sensitivity are performance measurements of interface predictions (see Supporting Information Text S3 for definitions). The higher their values, the more reliable the predictions.