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. 2015 Jul 1;43(W1):W408-12.
doi: 10.1093/nar/gkv451. Epub 2015 May 5.

CCTOP: a Consensus Constrained TOPology prediction web server

László Dobson  1 , István Reményi  1 , Gábor E Tusnády  2
Affiliations

CCTOP: a Consensus Constrained TOPology prediction web server

László Dobson et al. Nucleic Acids Res. .

Abstract

The Consensus Constrained TOPology prediction (CCTOP; http://cctop.enzim.ttk.mta.hu) server is a web-based application providing transmembrane topology prediction. In addition to utilizing 10 different state-of-the-art topology prediction methods, the CCTOP server incorporates topology information from existing experimental and computational sources available in the PDBTM, TOPDB and TOPDOM databases using the probabilistic framework of hidden Markov model. The server provides the option to precede the topology prediction with signal peptide prediction and transmembrane-globular protein discrimination. The initial result can be recalculated by (de)selecting any of the prediction methods or mapped experiments or by adding user specified constraints. CCTOP showed superior performance to existing approaches. The reliability of each prediction is also calculated, which correlates with the accuracy of the per protein topology prediction. The prediction results and the collected experimental information are visualized on the CCTOP home page and can be downloaded in XML format. Programmable access of the CCTOP server is also available, and an example of client-side script is provided.

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Figures

Figure 1.
Figure 1.
Correlation between the topology accuracy (in percent) of CCTOP and reliability. Predictions are sorted according to their reliability values, and then the topology accuracies and the lowest reliability measured on the subset of the benchmark set (red and magenta, respectively) are plotted against their rank in the sorted list divided by the number of the proteins in the benchmark set (coverage). Above 86% reliability value the prediction accuracy is expected to be 95%.
Figure 2.
Figure 2.
Layout of the result tabs of the CCTOP web server. (A) 2D tab (B) 3D tab. For details, see the text.
See this image and copyright information in PMC

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