ConPred_elite: A highly reliable approach to transmembrane topology prediction

Computational Biology and Chemistry

Volumn 28, Issue 1, 2004, Pages 51-60

  Xia, Jun Xiong ^a   Ikeda, Masami ^a,b   Shimizu, Toshio ^a  

^a HIROSAKI UNIVERSITY   (Japan)

^b IWATE UNIVERSITY   (Japan)

Author keywords

Consensus approach; High reliability; Proteome wide analysis; Transmembrane protein; Transmembrane topology prediction

Indexed keywords

BIOLOGICAL MEMBRANES; CLASSIFICATION (OF INFORMATION); GENES; GENETIC ENGINEERING; NUCLEAR MAGNETIC RESONANCE SPECTROSCOPY; TOPOLOGY; X RAY DIFFRACTION ANALYSIS;

PROTEOME WIDE ANALYSIS; SIGNAL PEPTIDES (SP); TRANSIT PEPTIDES (TP); TRANSMEMBRANE PROTEINS; TRANSMEMBRANE TOPOLOGY PREDICTION;

PROTEINS;

EUKARYOTA; PROKARYOTA;

ARCHAEAL PROTEIN; BACTERIAL PROTEIN; MEMBRANE PROTEIN; PROTEOME;

ARTICLE; CELL MEMBRANE; CHEMISTRY; CLASSIFICATION; COMPARATIVE STUDY; CONSENSUS SEQUENCE; EUKARYOTIC CELL; FACTUAL DATABASE; GENETICS; GENOME; PREDICTION AND FORECASTING; PROKARYOTIC CELL;

ARCHAEAL PROTEINS; BACTERIAL PROTEINS; CELL MEMBRANE; CONSENSUS SEQUENCE; DATABASES, FACTUAL; EUKARYOTIC CELLS; GENOME; MEMBRANE PROTEINS; PREDICTIVE VALUE OF TESTS; PROKARYOTIC CELLS; PROTEOME;

EID: 0842308529     PISSN: 14769271     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.compbiolchem.2003.11.002     Document Type: Article

References (33)

1. Arai M., Ikeda M., Shimizu T. Comprehensive analysis of transmembrane topologies in prokaryotic genomes. Gene. 304:2003;77-86.
2. Bahl A., Brunk B., Crabtree J., Fraunholz M.J., Gajria B., Grant G.R., Ginsburg H., Gupta D., Kissinger J.C., Labo P., Li L., Mailman M.D., Milgram A.J., Pearson D.S., Roos D.S., Schug J., Stoeckert C.J., Whetzel P. PlasmoDB: the plasmodium genome resource. A database integrating experimental and computational data. Nucleic Acids Res. 31:2003;212-215.
3. Benson D.A., Karsch-Mizrachi I., Lipman D.J., Ostell J., Wheeler D.L. GenBank. Nucleic Acids Res. 31:2003;23-27.
4. Boeckmann B., Bairoch A., Apweiler R., Blatter M.C., Estreicher A., Gasteiger E., Martin M.J., Michoud K., O'Donovan C., Phan I., Pilbout S., Schneider M. The SWISS-PROT protein knowledgebase and its supplement TrEMBL in 2003. Nucleic Acids Res. 31:2003;365-370.
5. Chen C.P., fKernytsky A., Rost B. Transmembrane helix predictions revisited. Protein Sci. 11:2002;2774-2791.
6. Clamp M., Andrews D., Barker D., Bevan P., Cameron G., Chen Y., Clark L., Cox T., Cuff J., Curwen V., Down T., Durbin R., Eyras E., Gilbert J., Hammond M., Hubbard T., Kasprzyk A., Keefe D., Lehvaslaiho H., Iyer V., Melsopp C., Mongin E., Pettett R., Potter S., Rust A., Schmidt E., Searle S., Slater G., Smith J., Spooner W., Stalker J., Stupka E., Ureta-Vidal A., Vastrik I., Birney E. Ensembl 2002: accommodating comparative genomics. Nucleic Acids Res. 31:2003;38-42.
7. Claros M.G., von Heijne G. TopPred II: an improved software for membrane protein structure predictions. Comput. Appl. Biosci. 10:1994;685-686.
8. Eisenberg D., Schwarz E., Komaromy M., Wall R. Analysis of membrane and surface protein sequences with the hydrophobic moment plot. J. Mol. Biol. 179:1984;125-142.
9. Hirokawa T., Boon-Chieng S., Mitaku S. SOSUI: classification and secondary structure prediction system for membrane proteins. Bioinformatics. 14:1998;378-379.
10. Hofmann K., Stoffel W. Tmbase - a database of membrane spanning proteins segments. Biol. Chem. Hoppe-Seyler. 347:1993;166.
11. Ikeda M., Arai M., Lao D.M., Shimizu T. Transmembrane topology prediction methods: a re-assessment and improvement by a consensus method using a dataset of experimentally-characterized transmembrane topologies. In Silico Biol. 2:2002;19-33.
12. Ikeda M., Arai M., Okuno T., Shimizu T. TMPDB: a database of experimentally-characterized transmembrane topologies. Nucleic Acids Res. 31:2003;406-409.
13. Jones D.T., Taylor W.R., Thornton J.M. A model recognition approach to the prediction of all-helical membrane protein structure and topology. Biochemistry. 33:1994;3038-3049.
14. Käll L., Sonnhammer E.L. Reliability of transmembrane predictions in whole-genome data. FEBS Lett. 532:2002;415-418.
15. Kehres D.G., Lawyer C.H., Maguire M.E. The CorA magnesium transporter gene family. Microb. Comp. Genom. 3:1998;151-169.
16. Krogh A., Larsson B., von Heijne G., Sonnhammer E.L. Predicting transmembrane protein topology with a hidden Markov model: application to complete genomes. J. Mol. Biol. 305:2001;567-580.
17. Lao, D.M., Shimizu, T., 2001. A method for discriminating a signal peptide and a putative 1st transmembrane segment. In: Valafar, F. (Ed.), Proceedings of 2001 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences (METMBS'01), CSREA Press, Las Vegas, pp. 119-125.
18. Lao D.M., Arai M., Ikeda M., Shimizu T. The presence of signal peptide significantly affects transmembrane topology prediction. Bioinformatics. 18:2002;1562-1566.
19. Lao D.M., Okuno T., Shimizu T. Evaluating transmembrane topology prediction methods for the effect of signal peptide in topology prediction. In Silico Biol. 2:2003;485-494.
20. Liu J., Rost B. Comparing function and structure between entire proteomes. Protein Sci. 10:2001;1970-1979.
21. Möller S., Croning M.D., Apweiler R. Evaluation of methods for the prediction of membrane spanning regions. Bioinformatics. 17:2001;646-653.
22. Ng P.C., Henikoff J.G., Henikoff S. PHAT: a transmembrane-specific substitution matrix. Predicted hydrophobic and transmembrane. Bioinformatics. 16:2000;760-766.
23. Nilsson J., Persson B., von Heijne G. Consensus predictions of membrane protein topology. FEBS Lett. 486:2000;267-269.
24. Nilsson J., Persson B., von Heijne G. Prediction of partial membrane protein topologies using a consensus approach. Protein Sci. 11:2002;2974-2980.
25. Ota K., Sakaguchi M., von Heijne G., Hamasaki N., Mihara K. Forced transmembrane orientation of hydrophilic polypeptide segments in multispanning membrane proteins. Mol. Cell. 2:1998;495-503.
26. Persson B., Argos P. Prediction of membrane protein topology utilizing multiple sequence alignments. J. Protein Chem. 16:1997;453-457.
27. Smith R.L., Banks J.L., Snavely M.D., Maguire M.E. Sequence and topology of the CorA magnesium transport systems of Salmonella typhimurium and Escherichia coli. Identification of a new class of transport protein. J. Biol. Chem. 268:1993;14071-14080.
28. Sonnhammer, E.L., von Heijne, G., Krogh, A., 1998. A hidden Markov model for predicting transmembrane helices in protein sequences. In: Glasgow, J., Littlejohn, T., Major, F., Lathrop, R., Sankoff, D., Sensen, C. (Eds.), Proceedings of the Sixth International Conference on Intelligent System for Molecular Biology, AAAI Press, Menlo Park, California, pp. 175-182.
29. Sugiyama Y., Polulyakh N., Shimizu T. Identification of transmembrane protein functions by binary topology patterns. Protein Eng. 16:2003;479-488.
30. Thompson J.D., Higgins D.G., Gibson T.J. CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res. 22:1994;4673-4680.
31. Tusnady G.E., Simon I. Principles governing amino acid composition of integral membrane proteins: application to topology prediction. J. Mol. Biol. 283:1998;489-506.
32. Tusnady G.E., Simon I. The HMMTOP transmembrane topology prediction server. Bioinformatics. 17:2001;849-850.
33. von Heijne G. Principles of membrane protein assembly and structure. Prog. Biophys. Mol. Biol. 66:1997;113-139.