Results obtained running waveTM, PRED-TMR, HMMTOP and TMHMM on various test sets



Test set Number of proteins Method used Qa Ca Qp TP FP FN
101 PRED-TMR 101 waveTM 0.90 0.77 0.95 409 38 26
PRED-TMR 0.88 0.79 0.95 406 16 29
HMMTOP 2.0 0.91 0.82 0.97 433 23 2
TMHMM 2.0 0.92 0.83 0.98 426 14 9
ROST (HIGH-RESOLUTION) 36 waveTM 0.73 0.58 0.92 100 2 23
PRED-TMR 0.77 0.58 0.92 106 2 17
HMMTOP 2.0 0.82 0.67 0.95 114 5 9
TMHMM 2.0 0.83 0.68 0.92 110 7 13
ROST (LOW-RESOLUTION) 165 waveTM 0.90 0.75 0.94 663 63 61
PRED-TMR 0.86 0.77 0.93 647 33 77
HMMTOP 2.0 0.90 0.80 0.96 700 42 24
TMHMM 2.0 0.89 0.79 0.95 670 28 54
MÖLLER (A) 37 waveTM 0.82 0.64 0.95 114 7 5
PRED-TMR 0.80 0.65 0.94 109 4 10
HMMTOP 2.0 0.82 0.67 0.96 115 8 4
TMHMM 2.0 0.83 0.68 0.92 110 8 9
MÖLLER (A, B) 60 waveTM 0.85 0.68 0.95 250 18 23
PRED-TMR 0.83 0.69 0.94 248 15 25
HMMTOP 2.0 0.85 0.70 0.95 266 21 7
TMHMM 2.0 0.86 0.72 0.94 253 13 20
MÖLLER (A, B, C) 188 waveTM 0.88 0.73 0.94 790 69 74
PRED-TMR 0.85 0.73 0.93 776 47 88
HMMTOP 2.0 0.88 0.76 0.96 847 66 17
TMHMM 2.0 0.89 0.77 0.95 811 39 53
MÖLLER (NON-REDUNDANT) 148 waveTM 0.88 0.72 0.95 651 55 60
PRED-TMR 0.85 0.72 0.93 641 41 70
HMMTOP 2.0 0.88 0.75 0.96 695 51 16
TMHMM 2.0 0.88 0.75 0.94 654 36 57

101 PRED-TMR: The test set of the 101 non-homologous transmembrane proteins used by Pasquier et al. (Protein Eng. 1999, 12, 381-385)

ROST: The set of transmembrane proteins described by Chen et al. (Protein Science 2002, 11, 2774-2791)

MÖLLER: The set of transmembrane proteins described by Möller et al. (Bioinformatics 2000, 16, 1159-60)

Qa : Per residue accuracy (For definition see Pasquier et al., 1999)

Ca : Correlation coefficient (For definition see Pasquier et al., 1999)

Qp : Per segment accuracy (For definition see Pasquier et al., 1999)