CCTOP: a Consensus Constrained TOPology prediction web server

By László Dobson, István Reményi, Gábor E. Tusnády. Nucleic Acids Res., 2015

400 citations recorded by the source corpus.

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.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/55bb9e09a9ec32c6a15859e7377c28af3ab199e6

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In Genetics

1. Christoph Peters

In Molecular Biology

1. G. Lukács
2. Christoph Peters
3. Markus M. Geisler
4. T. Hegedűs
5. Tim Wang
6. Bianka Farkas

Citations in the corpus

• Topology Prediction of α-Helical Transmembrane Proteins (2016, methodology): “A similar approach has been applied in MetaTM [100] and CCTOP [101].”
• Ins and outs of AlphaFold2 transmembrane protein structure predictions (2022, methodology): “The data also contained CCTOP [16] (http:// cctop. enzim. ttk. mta. hu) predictions and their reliability values.”
• A Genome-Wide CRISPR Screen in Toxoplasma Identifies Essential Apicomplexan Genes (2016, positive): “Topology prediction was performed against several representative orthologs with CCTOP (Dobson et al., 2015) and in all cases arrived at the same prediction of four transmembrane domains with cytoplasmic N and C termini (Figure S4).”