Frequently Asked Questions

CCTOP

1. What is CCTOP?
   The CCTOP server is a web-based application providing transmembrane topology prediction, where CCTOP stands for Constrained Consensus TOPology Prediction. It utilizes 10 different state-of-the-art topology prediction methods, and automatically incorporates previously determined structural and topology information in its probabilistic framework of hidden Markov model. The topology prediction can be preceded by signal peptide prediction and transmembrane-globular protein discrimination if requested. More detailed information can be found in the manuscripts.
2. How can I cite CCTOP?
   The Human Transmembrane Proteome
   László Dobson, István Reményi and Gábor E. Tusnády (2015)
   Biology Direct, 10:31
   [Journal] [Medline] [PDF]
   
   CCTOP: A Consensus Constrained TOPology prediction web server
   László Dobson, István Reményi and Gábor E. Tusnády (2015)
   Nucleic Acids Research, Webserver issue (43)
   [Journal] [Medline] [PDF]
   
   
3. What is reliability of topology?
   

   The reliability of a topology prediction is based on the trained Hidden Markov Model of CCTOP and is calculated by summing up the posterior probabilities along the state path determined by the Viterbi algorithm. As it can be seen in the plot below, the measured reliability in the 3D benchmark set highly correlate with the prediction accuracy (more information can be found here, or in the manuscripts).

   

   Predictions are sorted according to their reliability, the topology accuracies and reliability measured on benchmark set (red and magenta, respectively) are plotted against coverage.

4. In what format can sequences be submitted to CCTOP?
   Sequences can be submitted either with one letter amino acid format as plain text or in FASTA format.