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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).

From: Prediction of amphipathic in-plane membrane anchors in monotopic proteins using a SVM classifier

  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