Table 2.

Results of different sets of features performed on both single and two-layer models

Features	Predictor	Qtotal	MCC	Qobserved	Qpredicted
PSS (PHD, Jpred, PROTEUS) PSSMs	Single	78.3	0.52	79.7	54.5
	Two-layer	81.1	0.51	64.8	61.7
PSS (PROTEUS) PSSMs	Single	80.8	0.58	84.1	58.0
	Two-layer	82.7	0.55	69.5	64.2
PSS (PROTEUS) PSSMs Predicted Shape Strings	Single	87.3	0.69	86.5	69.8
	Two-layer	87.2	0.66	75.9	73.8

Note: PSS refers to predicted secondary structure.