On filtering false positive transmembrane protein predictions

Protein Engineering

Volumn 15, Issue 9, 2002, Pages 745-752

  Cserzö, Miklos ^a   Eisenhaber, Frank ^b   Eisenhaber, Birgit ^b   Simon, Istvan ^c  

^a UNIVERSITY OF BIRMINGHAM   (United Kingdom)

^b RESEARCH INSTITUTE OF MOLECULAR PATHOLOGY   (Austria)

^c INSTITUTE OF EXPERIMENTAL MEDICINE   (Hungary)

Author keywords

Automated sequence database screening; DAS TMfilter; Genome sequence annotation; Transmembrane region prediction

Indexed keywords

MEMBRANE PROTEIN;

ACCURACY; ALGORITHM; ANALYTIC METHOD; ARTICLE; CHEMICAL MODIFICATION; PREDICTION; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN STRUCTURE; SEQUENCE ANALYSIS; STRUCTURE ANALYSIS; THREE DIMENSIONAL IMAGING; BIOLOGY; CHEMISTRY; GENETICS; PROTEIN DATABASE; PROTEIN ENGINEERING; SEQUENCE ALIGNMENT; STATISTICS;

ALGORITHMS; COMPUTATIONAL BIOLOGY; DATABASES, PROTEIN; MEMBRANE PROTEINS; PROTEIN ENGINEERING; SEQUENCE ALIGNMENT;

EID: 0036763207     PISSN: 02692139     EISSN: None     Source Type: Journal    
DOI: 10.1093/protein/15.9.745     Document Type: Article

References (41)

1. Altschul, S.F., Madden, T.L., Schaffer, A.A., Zhang, J., Zhang, Z., Miller, W. and Lipman, D.J. (1997) Nucleic Acids Res., 25, 3389-3402.
2. Bairoch, A. and Apweiler, R. (2000) Nucleic Acids Res., 28, 5-48.
3. Berman, H.M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T.N., Weissig, H., Shindyalov, I.N. and Bourne, P.E. (2000) Nucleic Acids Res., 28, 235-242.
4. Cserzö, M. and Simon, I. (1989) Int. J. Pept. Protein Res., 34, 184-195.
5. Cserzö, M., Bernassau, J.M., Simon, I. and Maigret, B. (1994) J. Mol. Biol., 243, 388-396.
6. Cserzö, M., Wallin, E., Simon, I., von Heijne, G. and Elofsson, A. (1997) Protein Eng., 10, 673-676.
7. Eisenhaber, B., Bork, P. and Eisenhaber, F. (1999) J. Mol. Biol., 292, 741-758.
8. Eisenhaber, B., Bork, P. and Eisenhaber, F. (2001) Protein Eng., 14, 17-25.
9. Eisenhaber, F., Persson, B. and Argos, P. (1995) Crit. Rev. Biochem. Mol. Biol., 30, 1-94.
10. Engelman, D.M., Steitz, T.A. and Goldman, A. (1986) Annu. Rev. Biophys. Biophys. Chem., 15, 321-353.
11. Hirokawa, T., Boon-Chieng, S. and Mitaku, S. (1998) Bioinformatics, 14, 378-379.
12. Hobohm, U. and Sander, C. (1994) Protein Sci., 3, 522-524.
13. Hucho, F., Gorne-Tschelnokow, U. and Strecker, A. (1994) Trends Biochem. Sci., 19, 383-387.
14. Jayasinghe, S., Hristova, K. and White, S.H. (2001) J. Mol. Biol., 312, 927-934.
15. Jones, D.T., Taylor, W.R. and Thornton, J.M. (1994) Biochemistry, 33, 3038-3049.
16. Juretic, D., Zucic, D., Lucic, B. and Trinajstic, N. (1998) Comput. Chem., 22, 279-294.
17. Krogh, A., Larsson, B., von Heijne, G. and Sonnhammer, E.L. (2001) J. Mol. Biol., 305, 567-580.
18. Kuhlbrandt, W., Wang, D.N. and Fujiyoshi, Y. (1994) Nature, 367, 614-621.
19. Kyte, J. and Doolittle, R.F. (1982) J. Mol. Biol., 157, 105-132.
20. Lakey, J.H. and Slatin, S.L. (2001) Curr. Top. Microbiol. Immunol., 257, 131-161.
21. McGuffin, L.J., Bryson, K. and Jones, D.T. (2000) Bioinformatics, 16, 404-405.
22. Moller, S., Kriventseva, E.V. and Apweiler, R. (2000) Bioinformatics, 16, 1159-1160.
23. Moller, S., Croning, M.D. and Apweiler, R. (2001) Bioinformatics, 17, 646-653.
24. Nakai, K., Kidera, A. and Kanehisa, M. (1988) Protein Eng., 2, 93-100.
25. Nikiforovich, G.V. (1998) Protein Eng., 11, 279-283.
26. Nilsson, J., Persson, B. and von Heijne, G. (2000) FEBS Lett., 486, 267-269.
27. Palliser, C.C. and Parry, D.A. (2001) Proteins, 42, 243-255.
28. Pasquier, C. and Hamodrakas, S.J. (1999) Protein Eng., 12, 631-634.
29. Pasquier, C., Promponas, V.J., Palaios, G.A., Hamodrakas, J.S. and Hamodrakas, S.J. (1999) Protein Eng., 12, 381-385.
30. Persson, B. and Argos, P. (1996) Protein Sci., 5, 363-371.
31. Picot, D., Loll, P.J. and Garavito, R.M. (1994) Nature, 367, 243-249.
32. Rost, B., Casadio, R., Fariselli, P. and Sander, C. (1995) Protein Sci., 4, 521-533.
33. Simon, I., Fiser, A. and Tusnady, G.E. (2001) Biochim. Biophys. Acta, 1549, 123-136.
34. Sonnhammer, E.L., von Heijne, G. and Krogh, A. (1998) Proc. Int. Conf. Intell. Syst. Mol. Biol., 6, 175-182.
35. Tompa, P., Tusnady, G.E., Cserzö, M. and Simon, I. (2001) Proc. Natl Acad. Sci. USA, 98, 4431-4436.
36. Tudos, E., Cserzö, M. and Simon, I. (1990) Int. J. Pept. Protein Res., 36, 236-239.
37. Tusnady, G.E. and Simon, I. (1998) J. Mol. Biol., 283, 489-506.
38. Tusnady, G.E. and Simon, I. (2001a) Bioinformatics, 17, 849-850.
39. Tusnady, G.E. and Simon, I. (2001b) J. Chem. Inf. Comput. Sci., 41, 364-368.
40. von Heijne, G. (1992) J. Mol. Biol., 225, 487-494.
41. Weiss, M.S. and Schulz, G.E. (1992) J. Mol. Biol., 227, 493-509.