ConPred II: a Consensus Prediction Method for Obtaining Transmembrane Topology Models with High Reliability

Overview

Journal Nucleic Acids Res

Publisher Oxford University Press

Specialty Biochemistry

Date 2004 Jun 25

PMID 15215417

Citations 82

Authors

Masafumi Arai

Hironori Mitsuke

Masami Ikeda

Jun-Xiong Xia

Takashi Kikuchi

Masanobu Satake

Toshio Shimizu

Affiliations

Soon will be listed here.

Abstract

ConPred II (http://bioinfo.si.hirosaki-u.ac.jp/~ConPred2/) is a server for the prediction of transmembrane (TM) topology [i.e. the number of TM segments (TMSs), TMS positions and N-tail location] based on a consensus approach by combining the results of several proposed methods. The ConPred II system is constructed from ConPred_elite and ConPred_all (previously named ConPred), proposed earlier by our group. The prediction accuracy of ConPred_elite is almost 100%, which is achieved by sacrificing the prediction coverage (20-30%). ConPred_all predicts TM topologies for all the input sequences with accuracies improved by up to 11% over individual proposed methods. In the ConPred II system, the TM topology prediction of input TM protein sequences is executed following a two-step process: (i) input sequences are first run through the ConPred_elite program; (ii) sequences for which ConPred_elite does not give the TM topology are delivered to the ConPred_all program for TM topology prediction. Users can get access to the ConPred II system automatically by submitting sequences to the server. The ConPred II server will return the predicted TM topology models and graphical representations of their contents (hydropathy plots, helical wheel diagrams of predicted TMSs and snake-like diagrams).

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References

Ikeda M, Arai M, Okuno T, Shimizu T . TMPDB: a database of experimentally-characterized transmembrane topologies. Nucleic Acids Res. 2003; 31(1):406-9. PMC: 165467. DOI: 10.1093/nar/gkg020. View

Ikeda M, Arai M, Lao D, 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. 2002; 2(1):19-33. View

Moller S, Croning M, Apweiler R . Evaluation of methods for the prediction of membrane spanning regions. Bioinformatics. 2001; 17(7):646-53. DOI: 10.1093/bioinformatics/17.7.646. View

Claros M, von Heijne G . TopPred II: an improved software for membrane protein structure predictions. Comput Appl Biosci. 1994; 10(6):685-6. DOI: 10.1093/bioinformatics/10.6.685. View

Tusnady G, Simon I . The HMMTOP transmembrane topology prediction server. Bioinformatics. 2001; 17(9):849-50. DOI: 10.1093/bioinformatics/17.9.849. View

Cserzo M, Wallin E, Simon I, von Heijne G, Elofsson A . Prediction of transmembrane alpha-helices in prokaryotic membrane proteins: the dense alignment surface method. Protein Eng. 1997; 10(6):673-6. DOI: 10.1093/protein/10.6.673. View

Chen C, Kernytsky A, Rost B . Transmembrane helix predictions revisited. Protein Sci. 2002; 11(12):2774-91. PMC: 2373751. DOI: 10.1110/ps.0214502. View

Lao D, Arai M, Ikeda M, Shimizu T . The presence of signal peptide significantly affects transmembrane topology prediction. Bioinformatics. 2002; 18(12):1562-6. DOI: 10.1093/bioinformatics/18.12.1562. View

Arai M, Ikeda M, Shimizu T . Comprehensive analysis of transmembrane topologies in prokaryotic genomes. Gene. 2003; 304:77-86. DOI: 10.1016/s0378-1119(02)01181-2. View

10.

Xia J, Ikeda M, Shimizu T . ConPred_elite: a highly reliable approach to transmembrane topology predication. Comput Biol Chem. 2004; 28(1):51-60. DOI: 10.1016/j.compbiolchem.2003.11.002. View

11.

Jones D, Taylor W, Thornton J . A model recognition approach to the prediction of all-helical membrane protein structure and topology. Biochemistry. 1994; 33(10):3038-49. DOI: 10.1021/bi00176a037. View

12.

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

13.

Inoue Y, Ikeda M, Shimizu T . Proteome-wide classification and identification of mammalian-type GPCRs by binary topology pattern. Comput Biol Chem. 2004; 28(1):39-49. DOI: 10.1016/j.compbiolchem.2003.11.003. View

14.

Hirokawa T, Mitaku S . SOSUI: classification and secondary structure prediction system for membrane proteins. Bioinformatics. 1998; 14(4):378-9. DOI: 10.1093/bioinformatics/14.4.378. View

15.

Persson B, Argos P . Prediction of membrane protein topology utilizing multiple sequence alignments. J Protein Chem. 1997; 16(5):453-7. DOI: 10.1023/a:1026353225758. View

16.

Klein P, Kanehisa M, Delisi C . The detection and classification of membrane-spanning proteins. Biochim Biophys Acta. 1985; 815(3):468-76. DOI: 10.1016/0005-2736(85)90375-x. View

17.

Sugiyama Y, Polulyakh N, Shimizu T . Identification of transmembrane protein functions by binary topology patterns. Protein Eng. 2003; 16(7):479-88. DOI: 10.1093/protein/gzg068. View