Bioinformatics Vol. 17 no. 7 2001
Pages 646-653
© 2001 Oxford University Press
Evaluation of methods for the prediction of membrane spanning regions
1 EMBL-Outstation European Bioinformatics
Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10
1SD, UK
2 School of Biological Sciences, The
University of Manchester, Oxford Road, Manchester M13 9PT, UK
Received on December 15, 2000
; revised on March 13, 2001
; accepted on March 16, 2001
Motivation: A variety of tools are available to predict the topology of transmembrane proteins. To date no independent evaluation of the performance of these tools has been published. A better understanding of the strengths and weaknesses of the different tools would guide both the biologist and the bioinformatician to make better predictions of membrane protein topology.
Results: Here we present an evaluation of the performance of the currently best known and most widely used methods for the prediction of transmembrane regions in proteins. Our results show that TMHMM is currently the best performing transmembrane prediction program.
Contact: moeller{at}ebi.ac.uk; croning{at}ebi.ac.uk; apweiler{at}ebi.ac.uk
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 J. F. Kreuze, E. I. Savenkov, and J. P. T. Valkonen Complete Genome Sequence and Analyses of the Subgenomic RNAs of Sweet Potato Chlorotic Stunt Virus Reveal Several New Features for the Genus Crinivirus J. Virol., August 12, 2002; 76(18): 9260 - 9270. [Abstract] [Full Text] [PDF]
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R. Mott, J. Schultz, P. Bork, and C. P. Ponting Predicting Protein Cellular Localization Using a Domain Projection Method Genome Res., August 1, 2002; 12(8): 1168 - 1174. [Abstract] [Full Text] [PDF]
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 X. Zhang, K. K. Evans, and S. H. Wright Molecular cloning of rabbit organic cation transporter rbOCT2 and functional comparisons with rbOCT1 Am J Physiol Renal Physiol, July 1, 2002; 283(1): F124 - F133. [Abstract] [Full Text] [PDF]
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A. Weihofen, K. Binns, M. K. Lemberg, K. Ashman, and B. Martoglio Identification of Signal Peptide Peptidase, a Presenilin-Type Aspartic Protease Science, June 21, 2002; 296(5576): 2215 - 2218. [Abstract] [Full Text] [PDF]
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E. Bertaccini and J.R. Trudell Predicting the transmembrane secondary structure of ligand-gated ion channels Protein Eng. Des. Sel., June 1, 2002; 15(6): 443 - 453. [Abstract] [Full Text] [PDF]
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R. Dorenbos, T. Stein, J. Kabel, C. Bruand, A. Bolhuis, S. Bron, W. J. Quax, and J. M. van Dijl Thiol-Disulfide Oxidoreductases Are Essential for the Production of the Lantibiotic Sublancin 168 J. Biol. Chem., May 3, 2002; 277(19): 16682 - 16688. [Abstract] [Full Text] [PDF]
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J. M. Morante-Redolat, A. Gorostidi-Pagola, S. Piquer-Sirerol, A. Saenz, J. J. Poza, J. Galan, S. Gesk, T. Sarafidou, V.-F. Mautner, S. Binelli, et al. Mutations in the LGI1/Epitempin gene on 10q24 cause autosomal dominant lateral temporal epilepsy Hum. Mol. Genet., May 1, 2002; 11(9): 1119 - 1128. [Abstract] [Full Text] [PDF]
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J. Isosomppi, J. Vesa, A. Jalanko, and L. Peltonen Lysosomal localization of the neuronal ceroid lipofuscinosis CLN5 protein Hum. Mol. Genet., April 15, 2002; 11(8): 885 - 891. [Abstract] [Full Text] [PDF]
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D. Drew, D. Sjostrand, J. Nilsson, T. Urbig, C.-n. Chin, J.-W. de Gier, and G. von Heijne Rapid topology mapping of Escherichia coli inner-membrane proteins by prediction and PhoA/GFP fusion analysis PNAS, February 20, 2002; (2002) 52018199. [Abstract] [Full Text] [PDF]
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D. Drew, D. Sjostrand, J. Nilsson, T. Urbig, C.-n. Chin, J.-W. de Gier, and G. von Heijne Rapid topology mapping of Escherichia coli inner-membrane proteins by prediction and PhoA/GFP fusion analysis PNAS, March 5, 2002; 99(5): 2690 - 2695. [Abstract] [Full Text] [PDF]
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