CCTOP: a Consensus Constrained TOPology Prediction Web Server

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2015 May 7

PMID 25943549

Citations 193

Authors

Laszlo Dobson

Istvan Remenyi

Gabor E Tusnady

Affiliations

Soon will be listed here.

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.

Citing Articles

Structural and Functional Analysis of the Lectin-like Protein Llp1 Secreted by upon Infection of Maize.

Christ M, Rubio Elizalde I, Weiland P, Kern A, Iwen T, Mais C J Fungi (Basel). 2025; 11(2).

PMID: 39997458 PMC: 11857070. DOI: 10.3390/jof11020164.

Integrons are anti-phage defence libraries in Vibrio parahaemolyticus.

Getz L, Fairburn S, Vivian Liu Y, Qian A, Maxwell K Nat Microbiol. 2025; 10(3):724-733.

PMID: 39870871 DOI: 10.1038/s41564-025-01927-7.

Genome-wide analysis and characterization of TPD1 family proteins in pearl millet (Cenchrus americanus): Insights into reproductive regulation and phytohormone responses.

Almutairi Z PLoS One. 2025; 20(1):e0318196.

PMID: 39869569 PMC: 11771933. DOI: 10.1371/journal.pone.0318196.

Elucidating assembly and function of VirB8 cell wall subunits refines the DNA translocation model in Gram-positive T4SSs.

Maffo-Woulefack R, Ali A, Laroussi H, Cappele J, Romero-Saavedra F, Ramia N Sci Adv. 2025; 11(4):eadq5975.

PMID: 39841841 PMC: 11753425. DOI: 10.1126/sciadv.adq5975.

Computational Insights on the Assembly of the Dengue Virus Membrane-Capsid-RNA Complex.

Chaudhuri D, Majumder S, Datta J, Giri K J Membr Biol. 2025; 258(1):75-96.

PMID: 39827433 DOI: 10.1007/s00232-025-00337-4.

References

Sokolowska I, Ngounou Wetie A, Roy U, Woods A, Darie C . Mass spectrometry investigation of glycosylation on the NXS/T sites in recombinant glycoproteins. Biochim Biophys Acta. 2013; 1834(8):1474-83. DOI: 10.1016/j.bbapap.2013.04.022. View

Das S, Hahn Y, Walker D, Nagata S, Willingham M, Peehl D . Topology of NGEP, a prostate-specific cell:cell junction protein widely expressed in many cancers of different grade level. Cancer Res. 2008; 68(15):6306-12. PMC: 2562772. DOI: 10.1158/0008-5472.CAN-08-0870. View

Dobson L, Remenyi I, Tusnady G . The human transmembrane proteome. Biol Direct. 2015; 10:31. PMC: 4445273. DOI: 10.1186/s13062-015-0061-x. View

KROGH A, Larsson B, von Heijne G, Sonnhammer E . Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J Mol Biol. 2001; 305(3):567-80. DOI: 10.1006/jmbi.2000.4315. View

Shen H, Chou J . MemBrain: improving the accuracy of predicting transmembrane helices. PLoS One. 2008; 3(6):e2399. PMC: 2396505. DOI: 10.1371/journal.pone.0002399. View

Wang H, He Z, Zhang C, Zhang L, Xu D . Transmembrane protein alignment and fold recognition based on predicted topology. PLoS One. 2013; 8(7):e69744. PMC: 3716705. DOI: 10.1371/journal.pone.0069744. View

Sonnhammer E, von Heijne G, KROGH A . A hidden Markov model for predicting transmembrane helices in protein sequences. Proc Int Conf Intell Syst Mol Biol. 1998; 6:175-82. View

Trinidad J, Schoepfer R, Burlingame A, Medzihradszky K . N- and O-glycosylation in the murine synaptosome. Mol Cell Proteomics. 2013; 12(12):3474-88. PMC: 3861701. DOI: 10.1074/mcp.M113.030007. View

Heijne G . The distribution of positively charged residues in bacterial inner membrane proteins correlates with the trans-membrane topology. EMBO J. 1986; 5(11):3021-7. PMC: 1167256. DOI: 10.1002/j.1460-2075.1986.tb04601.x. View

10.

Tusnady G, Dosztanyi Z, Simon I . Transmembrane proteins in the Protein Data Bank: identification and classification. Bioinformatics. 2004; 20(17):2964-72. DOI: 10.1093/bioinformatics/bth340. View

11.

Bagos P, Liakopoulos T, Hamodrakas S . Algorithms for incorporating prior topological information in HMMs: application to transmembrane proteins. BMC Bioinformatics. 2006; 7:189. PMC: 1523218. DOI: 10.1186/1471-2105-7-189. View

12.

Wang G, Wu Y, Zhou T, Guo Y, Zheng B, Wang J . Mapping of the N-linked glycoproteome of human spermatozoa. J Proteome Res. 2013; 12(12):5750-9. DOI: 10.1021/pr400753f. View

13.

Viklund H, Elofsson A . Best alpha-helical transmembrane protein topology predictions are achieved using hidden Markov models and evolutionary information. Protein Sci. 2004; 13(7):1908-17. PMC: 2279939. DOI: 10.1110/ps.04625404. View

14.

Petersen T, Brunak S, von Heijne G, Nielsen H . SignalP 4.0: discriminating signal peptides from transmembrane regions. Nat Methods. 2011; 8(10):785-6. DOI: 10.1038/nmeth.1701. View

15.

Brach T, Soyk S, Muller C, Hinz G, Hell R, Brandizzi F . Non-invasive topology analysis of membrane proteins in the secretory pathway. Plant J. 2008; 57(3):534-41. DOI: 10.1111/j.1365-313X.2008.03704.x. View

16.

Li W, Godzik A . Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics. 2006; 22(13):1658-9. DOI: 10.1093/bioinformatics/btl158. View

17.

Bernsel A, Viklund H, Falk J, Lindahl E, von Heijne G, Elofsson A . Prediction of membrane-protein topology from first principles. Proc Natl Acad Sci U S A. 2008; 105(20):7177-81. PMC: 2438223. DOI: 10.1073/pnas.0711151105. View

18.

Arai M, Mitsuke H, Ikeda M, Xia J, Kikuchi T, Satake M . ConPred II: a consensus prediction method for obtaining transmembrane topology models with high reliability. Nucleic Acids Res. 2004; 32(Web Server issue):W390-3. PMC: 441518. DOI: 10.1093/nar/gkh380. View

19.

Charbit A, RONCO J, Michel V, Werts C, Hofnung M . Permissive sites and topology of an outer membrane protein with a reporter epitope. J Bacteriol. 1991; 173(1):262-75. PMC: 207183. DOI: 10.1128/jb.173.1.262-275.1991. View

20.

Tusnady G, Simon I . Principles governing amino acid composition of integral membrane proteins: application to topology prediction. J Mol Biol. 1998; 283(2):489-506. DOI: 10.1006/jmbi.1998.2107. View