Table 1

Obtained accuracy of the predictors, in a test set of 20 outer membrane proteins

METHOD

TYPE

SEQUENCE

Qβ

Cβ

SOV

Correctly predicted topologies

Correctly predicted barrel size


HMM-B2TMR

HMM

barrel

0.737

0.557

0.836

15

17

precursor

0.790

0.600

0.813

14

16

ProfTMB

HMM

barrel

0.734

0.537

0.818

14

17

precursor

0.777

0.575

0.784

12

16

PRED-TMBBpost

HMM

barrel

0.818

0.630

0.886

14

19

precursor

0.842

0.637

0.852

14

16

PRED-TMBBnbest

HMM

barrel

0.818

0.629

0.877

12

17

precursor

0.849

0.637

0.856

11

13

TBBPred-comb

NN+SVM

barrel

0.702

0.428

0.664

0

0

precursor

0.701

0.424

0.496

0

0

TBBPred-nn

NN

barrel

0.735

0.466

0.672

0

1

precursor

0.726

0.432

0.496

0

1

TBBPred-svm

SVM

barrel

0.744

0.458

0.721

1

3

precursor

0.744

0.426

0.535

0

0

B2TMPRED

NN

barrel

0.723

0.498

0.738

7

9

precursor

0.709

0.466

0.551

0

0

TMBETA-NET

HMM

barrel

0.697

0.415

0.698

3

8

precursor

0.663

0.353

0.515

0

4

BETA-TM

NN

barrel

0.690

0.395

0.691

1

2

precursor

0.663

0.322

0.497

0

1

PSI-PRED

NN

barrel

0.731

0.484

0.690

0

0

precursor

0.756

0.495

0.569

0

0

HMM-B2TMR, ProfTMB, PRED-TMBBpost, B2TMPRED, TBBPred-nn

CONSENSUS

barrel

0.819

0.641

0.924

18

20

precursor

0.849

0.660

0.874

15

18


For an explanation of the measures of accuracy see the Materials and Methods section. Abbreviations: PRED-TMBBpost: PRED-TMBB method with posterior decoding, PRED-TMBBnbest: PRED-TMBB method with NBest decoding, TBBPred-nn: The Neural Network module of TBBPred, TBBPred-svm: The SVM module of TBBPred, TBBPred-comb: TBBPred, combining the Neural Network and SVM modules. The performance of the best individual predictor, and the best available consensus obtained are highlighted with bold.

Bagos et al. BMC Bioinformatics 2005 6:7   doi:10.1186/1471-2105-6-7

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