ZPRED: Predicting the distance to the membrane center for residues in α-helical membrane proteins

Bioinformatics

Volumn 22, Issue 14, 2006, Pages

  Granseth, Erik ^a   Viklund, Håkan ^a   Elofsson, Arne ^a  

^a STOCKHOLM UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

GLUTAMATE TRANSPORTER; HELIX LOOP HELIX PROTEIN; MEMBRANE PROTEIN;

ACCURACY; ALPHA HELIX; ANALYTICAL ERROR; ARTIFICIAL NEURAL NETWORK; CONFERENCE PAPER; NONHUMAN; PREDICTION; PRIORITY JOURNAL; PROBABILITY; PROTEIN ANALYSIS; PROTEIN LOCALIZATION; PYROCOCCUS HORIKOSHII; STATISTICAL MODEL;

EID: 33747871503     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btl206     Document Type: Conference Paper

References (26)

1. Altschul,S.F., Gish,W., Miller,W., Myers,E.W. and Lipman,D.J. (1990) Basic local alignment search tool. J. Mol. Biol., 215, 403-410.
2. Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: A new generation of protein database search programs. Nucleic Acids Res., 25, 3389-3402.
3. Berman,H.M., Westbrook,J., Feng,Z., Gilliland,G., Bhat,T.N. and Weissig,H. (2000) The protein data bank. Nucleic Acids Res., 28, 235-242.
4. Bishop,C.M. (1995) Neural networks for pattern recognition. Oxford university press.
5. Chen,C.P. and Rost,B. (2002) State-of-the-art in membrane protein prediction. Appl. Bioinformatics, 1, 21-35.
6. Chen,C.P., Kernytsky,A. and Rost,B. (2002) Transmembrane helix predictions revisited. Protein Sci., 11, 2774-2791.
7. Engelman,D.M., Steitz,T.A. and Goldman,A. (1986) Identifying nonpolar transbilayer helices in amino acid sequences of membrane proteins. Annu. Rev. Biophys. Biophys. Chem., 15, 321-353.
8. Granseth,E., Daley,D.O., Rapp,M., Melen,K. and von Heijne,G. (2005a) Experimentally constrained topology models for 51,208 bacterial inner membrane proteins. J. Mol. Biol., 352, 489-494.
9. Granseth,E., von Heijne,G. and Elofsson,A. (2005b) A study of the membrane-water interface region of membrane proteins. J. Mol. Biol., 346, 377-385.
10. Hedman,M., Deloof,H., von Heijne,G. and Elofsson,A. (2002) Improved detection of homologous membrane proteins by inclusion of information from topology prediction. Protein Sci., 11, 652-658.
11. Käll,L. and Sonnhammer,E.L. (2002) Reliability of transmembrane predictions in whole-genome data. FEBS Lett., 532, 415-418.
12. Krogh,A., Larsson,B., von Heijne,G. and Sonnhammer,E.L. (2001) Predicting transmembrane protein topology with a hidden Markov model: Application to complete genomes. J. Mol. Biol., 305, 567-580.
13. Popov,M., Tam,L.Y., Li,J. and Reithmeier,R.A. (1997) Mapping the ends of trans-membrane segments in a polytopic membrane protein. scanning N-glycosylation mutagenesis of extracytosolic loops in the anion exchanger, band 3. J. Biol. Chem., 272, 18325-18332.
14. Sonnhammer,E.L., von Heijne,G. and Krogh,A. (1998) A hidden markov model for predicting transmembrane helices in protein sequences. Proc. Int. Conf. Intell. Syst. Mol. Biol., 6, 175-182.
15. Taylor,W.R., Jones,D.T. and Green,N.M. (1994) A method for alpha-helical integral membrane protein fold prediction. Proteins, 18, 281-294.
16. Tornroth-Horsefield,S., Wang,Y., Hedfalk,K., Johanson,U., Karlsson,M., Tajkhorshid,E., Neutze,R. and Kjellbom,P. (2006) Structural mechanism of plant aquaporin gating. Nature, 439, 688-694.
17. Tusnády,G.E., Dosztanyi,Z. and Simon,I. (2005) TMDET: Web server for detecting transmembrane regions of proteins by using their 3d coordinates. Bioinformatics, 21, 1276-1277.
18. Tusnády,G.E. and Simon,I. (1998) Principles governing amino acid composition of integral membrane proteins: Application to topology prediction. J. Mol. Biol., 283, 489-506.
19. Tusnády,G.E. and Simon,I. (2001) The HMMTOP transmembrane topology prediction server. Bioinformatics, 17, 849-850.
20. Viklund,H. and Elofsson,A. (2004) Best alpha-helical transmembrane protein topology predictions are achieved using hidden markov models and evolutionary information. Protein Sci., 13, 1908-1917.
21. von Heijne,G. (1986) The distribution of positively charged residues in bacterial inner membrane proteins correlates with the trans-membrane topology. EMBO J., 5, 3021-3027.
22. von Heijne,G. (1992) Membrane protein structure prediction. Hydrophobicity analysis and the positive-inside rule. J. Mol. Biol., 225, 487-494.
23. von Heijne,G. (1994) Membrane proteins: From sequence to structure. Biophys. Biomol. Struct., 23, 167-192.
24. White,S.H. (2004) The progress of membrane protein structure determination. Protein Sci., 13, 1948-1949.
25. White,S.H. and Wimley,W.C. (1999) Membrane protein folding and stability: Physical principles. Annu. Rev. Biophys. Biomol. Struct., 28, 319-365.
26. Yernool,D., Boudker,O., Jin,Y. and Gouaux,E. (2004) Structure of a glutamate transporter homologue from Pyrococcus horikoshii. Nature, 431, 811-818. E.Granseth et al.