Identification of transmembrane protein functions by binary topology patterns

Protein Engineering

Volumn 16, Issue 7, 2003, Pages 479-488

  Sugiyama, Yoshiaki ^a   Polulyakh, Natalia ^a,b   Shimizu, Toshio ^a  

^a HIROSAKI UNIVERSITY   (Japan)

^b OCHANOMIZU UNIVERSITY   (Japan)

Author keywords

Binary topology pattern; Functional identification; Loop length; Transmembrane protein; Transmembrane topology

Indexed keywords

MEMBRANE PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; BINARY TOPOLOGY PATTERN; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN FUNCTION; PROTEIN STRUCTURE; SENSITIVITY AND SPECIFICITY;

EID: 0042880963     PISSN: 02692139     EISSN: None     Source Type: Journal    
DOI: 10.1093/protein/gzg068     Document Type: Article

References (30)

1. Anand, R. (2000) Biochem. Biophys. Res. Commun., 276, 157-161.
2. Arai, M., Ikeda, M. and Shimizu, T. (2002) Gene, 304, 77-86.
3. Bairoch, A. and Apweiler, R. (2000) Nucleic Acids Res., 28, 45-48.
4. Bertaccini, E. and Trudell, J. R. (2002) Protein Eng., 15, 443-453.
5. Chen, C.P., Kernytsky, A. and Rost, B. (2002) Protein Sci., 11, 2774-2791.
6. Claros, M.G. and von Heijne, G. (1994) Comput. Appl. Biosci., 10, 685-686.
7. Clements, J.D. and Martin, R.D. (2002) Eur. J. Biochem., 269, 2101-2107.
8. Hirokawa, T., Boon-Chieng, S. and Miraku, S. (1998) Bioinformatics, 14, 378-379.
9. Hollmann, M., Maron, C. and Heinemann, S. (1994) Neuron, 13, 1331-1343.
10. Ikeda, M., Arai, M., Lao, D.M. and Shimizu, T. (2002) In Silico Biol., 2, 19-33.
11. Ikeda, M., Arai, M., Okuno, T. and Shimizu, T. (2003) Nucleic Acids Res., 31, 406-409.
12. Jones, D.T. (1998) FEBS Lett., 423, 281-285.
13. Jones, D.T., Taylor, W.R. and Thomton, J.M. (1994) Biochemistry, 33, 3038-3049.
14. Kall, L. and Sonnhammer, E.L.L. (2002) FEBS Lett., 532, 415-418.
15. Krogh, A., Larsson, B., von Heijne, G. and Sonnhammer, E.L.L. (2001) J. Mol. Biol., 305, 567-580.
16. Liu, J. and Rost, B. (2001) Protein Sci., 10, 1970-1979.
17. Mitaku, S., Ono, M., Hirokawa, T., Boon-Chieng, S. and Sonoyama, M. (1999) Biophys. Chem., 82, 165-171.
18. Moeller, S., Croning, M.D.R. and Apweiler, R. (2001) Bioinformatics, 17, 646-653.
19. Nilsson, J., Persson, B. and von Heijne, G. (2000) FEBS Lett., 486, 267-269.
20. Nilsson, J., Persson, B. and von Heijne, G. (2002) Protein Sci., 11, 2974-2980.
21. Otaki, J.M. and Firestein, S. (2001) J. Theor. Biol., 211, 77-100.
22. Promponas, V.J., Palaios, G.A., Pasquier, C.M., Hamodrakas, J.S. and Hamodrakas, S.J. (1999) In Silico Biol., 1, 159-162.
23. Rost, B., Casadio, R. and Fariselli, P. (1996) In States, D.T., Agarwal, P., Gaasterland, T., Hunter, L. and Smith, R.F. (eds), Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA, pp. 192-200.
24. Serres, M.H., Gopal, S., Nahum, L.A., Liang, P., Gaasterland, T. and Riley, M. (2001) Genome Biol., 2, research0035.1-0035.7.
25. Sonnhammer, E.L., von Heijne, G. and Krogh, A. (1998) In Glasgow, J., Littlejohn, T., Major, F., Lathrop, R., Sankoff, D. and Sensen, C. (eds), Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology. AAAI Press, Menlo Park, CA, pp. 175-182.
26. Stevens, T.J. and Arkin, I.T. (2000) Proteins: Struct. Funct. Genet., 39, 417-420.
27. Tusnady, G.E. and Simon, I. (1998) J. Mol. Biol., 283, 489-506.
28. Tusnady, G.E., Bakos, E., Varadi, A. and Sarkadi, B. (1997) FEBS Lett., 402, 1-3.
29. Wallin, E. and von Heijne, G. (1998) Protein Sci., 7, 1029-1038.
30. Yoshizaki, G., Patino, P. and Thomas, P. (1994) Biol. Reprod., 51, 493-503.