Table 1. Prediction accuracy (in percent) of the CCTOP compared with the accuracies of the incorporated methods, as well as two consensus methods (TOPCONS and MetaTM) on the newly compiled benchmark set containing 170 proteins.

	CCTOP*	CCTOP	HMMTOP*	MemBrain	MEMSAT-SVM	MetaTM	Octopus	Philius	Phobius	Pro	Prodiv	Scampi-MSA	TMHMM	TOPCONS
Sens/res	98	98	95	92	94	94	93	95	93	96	96	97	93	97
Spec/res	98	98	95	97	98	97	98	97	97	97	95	97	97	98
MCC/res	98	98	95	95	96	96	96	96	95	97	96	97	95	97
AccTpg/prot	84	84	69	62	66	67	71	71	62	75	75	76	66	79
AccTop/prot	81	79	64	0	53	58	66	64	56	70	69	72	59	75

Predictions marked with * are enhanced with topological constraints from TOPDB and TOPDOM databases. Structural information from PDBTM was not used in any of these tests. Sens/res is the per residues sensitivity, Spec/res is the per residue specificity, MCC/res is the Matthew correlation coefficient, Acc_Tpg/prot is the per protein topography accuracy, Acc_Tpl/prot is the per protein topology accuracy.