Evaluation of methods for predicting the topology of β-barrel outer membrane proteins and a consensus prediction method

Table 4 Obtained accuracy of the consensus predictions, in the test set of 20 outer membrane proteins

METHOD	TYPE	SEQUENCE	Q_β	C_β	SOV	Correctly predicted topologies	Correctly predicted barrel size
PRED-TMBB, ProfTMB, HMM-B2TMR	CONSENSUS	barrel	0.771	0.596	0.877	17	19
		precursor	0.818	0.628	0.86	15	18
PRED-TMBB, ProfTMB, HMM-B2TMR, B2TMPRED	CONSENSUS	barrel	0.790	0.616	0.896	17	19
		precursor	0.832	0.641	0.865	15	18
PRED-TMBB, ProfTMB, HMM-B2TMR, TBBPred-nn	CONSENSUS	barrel	0.809	0.635	0.917	18	20
		precursor	0.839	0.653	0.867	15	18
PRED-TMBB, ProfTMB, HMM-B2TMR, TBBPred-svm	CONSENSUS	barrel	0.809	0.629	0.906	15	19
		precursor	0.847	0.658	0.882	15	18
PRED-TMBB, ProfTMB, HMM-B2TMR, TBBPred-comb	CONSENSUS	barrel	0.791	0.607	0.894	17	20
		precursor	0.833	0.648	0.859	15	18
PRED-TMBB, ProfTMB, HMM-B2TMR, TBBPred-nn/svm	CONSENSUS	barrel	0.824	0.638	0.92	17	19
		precursor	0.85	0.647	0.871	13	17
PRED-TMBB, ProfTMB, HMM-B2TMR, B2TMPRED, TBBPred-nn/svm	CONSENSUS	barrel	0.825	0.637	0.927	17	18
		precursor	0.854	0.652	0.876	15	17
PRED-TMBB, ProfTMB, HMM-B2TMR, B2TMPRED, TBBPred-nn	CONSENSUS	barrel	0.819	0.641	0.924	18	20
		precursor	0.849	0.660	0.874	15	18
PRED-TMBB, ProfTMB, HMM-B2TMR, B2TMPRED, TBBPred-comb	CONSENSUS	barrel	0.807	0.625	0.907	17	19
		precursor	0.845	0.658	0.868	15	18
PRED-TMBB, ProfTMB, HMM-B2TMR, B2TMPRED, TBBPred-svm	CONSENSUS	barrel	0.819	0.637	0.910	15	19
		precursor	0.853	0.659	0.880	14	18
PRED-TMBB, ProfTMB, B2TMPRED, TBBPred-svm/nn	CONSENSUS	barrel	0.829	0.642	0.923	17	18
		precursor	0.851	0.648	0.861	15	16
PRED-TMBB, ProfTMB, B2TMPRED, TBBPred-svm, TBBPred-nn, HMM-B2TMR, TMBETA-NET, PSI-PRED, BETA-TM	CONSENSUS	barrel	0.808	0.582	0.851	11	13
		precursor	0.844	0.604	0.841	12	13

We report the consensus of all the available methods, and the ones that were obtained using the 3 top-scoring HMMs combined in various ways with some of the top-scoring NN/SVM methods. The best results are highlighted with bold. For abbreviations see also Table 1.

ISSN: 1471-2105