Table 4.

Classification performance for 3 sets of soluble or transmembrane proteins naively tested. "Observed as" corresponds to the number of residues observed at a TM or a non-TM position. "Predicted as" corresponds to the number of residues predicted at a IPM or non-IPM position. "Proteins with TM α-helix" is a set of 101 proteins with 1 or more TM α-helices. "Proteins with TM β-barrel" is a set of 21 TM β-barrel proteins. TM proteins are extracted from the MPtopo database (3D_helix and 3D_other subsets, respectively). "Soluble proteins" is a set of 65 soluble proteins extracted from the PDB (sequence similarity < 25%). These 3 sets were submitted to the sequence-to-topology SVM, using PHAT and a positional weighting (Table 1). An average prediction was then computed for each sequence of the sets following the procedure described above (Table 3).

	Proteins with TM α-helix		Proteins with TM β-barrel		Soluble proteins
	Observed as		Observed as		Observed as
Predicted as	TM	non-TM	TM	non-TM	TM	non-TM
IPM	181	152	16	5	-	57
non-IPM	11057	14423	3540	4138	-	30310
Total number of residues	11238	14575	3556	4143	-	30367