!title
Constrained Consensus TOPology prediction server

Description of the CCTOP server

Accuracy of the various methods and CCTOP on the benchmark set

The test was performed on a benchmark set containing 170 proteins with known structure. If experimental constraints from the PDBTM database would have been used, the test had resulted in 100% per protein prediction accuracy. Therefore, the topological constraints were not used in this test. Thus the real accuracy of CCTOP is above of these values.

Per protein topology accuracies

Prediction details

Method Sensitivity Specificity MCC AccTpg AccTpl
CCTOP989897.78481
TopCons9797.797.27975
ScampiMsa9796.796.87672
Pro9697.396.57570
Prodiv9694.895.57569
Octopus9398.295.77166
HMMTOP9594.794.86964
Philius959795.97164
TMHMM9397.294.96659
MetaTM949796.06758
Phobius9397.395.16256
Memsat949895.86653
MemBrain9297.494.7620

We estimated the helix boundaries accuracy by BLAST searching all sequences in the OPM database against itself, and compared the transmembrane segment boundaries of proteins, which have 40% or larger sequence similarity to each other. By using the same method, we measured the transmembrane segment boundaries difference between OPM and CCTOP, and got the same result (3.3±0.5 residues). Thus, CCTOP predicts helix boundaries as accurate as it can be determined from the 3D structures by biophysics based method. For comparison, we determined the helix boundaries prediction accuracies of the used methods as well:

MethodAverage distance
(residues)
OPM3.3±0.5
CCTOP3.3±0.5
Octopus3.6±0.3
Memsat3.6±0.6
PRODIV3.7±1.3
Scampi3.7±1.3
Phobius3.8±1.1
Philius3.8±0.9
PRO3.8±1.1
TMHMM3.9±0.9
Membrain4.0±1.0
HMMTOP4.2±0.7