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

CCTOP: a Consensus Constrained TOPology prediction web server.

Author information

1
'Momentum' Membrane Protein Bioinformatics Research Group, Institute of Enzymology, RCNS, HAS, Budapest PO Box 7, H-1518, Hungary.
2
'Momentum' Membrane Protein Bioinformatics Research Group, Institute of Enzymology, RCNS, HAS, Budapest PO Box 7, H-1518, Hungary tusnady.gabor@ttk.mta.hu.

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.

PMID:
25943549
PMCID:
PMC4489262
DOI:
10.1093/nar/gkv451
[Indexed for MEDLINE]
Free PMC Article

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