Structure optimization of an artificial neural filter detecting membrane-spanning amino acid sequences

Biopolymers

Volumn 38, Issue 1, 1996, Pages 13-29

  Lohmann, Reinhard ^a   Schneider, Gisbert ^b   Wrede, Paul ^b  

^a Haus 137   (Germany)

^b FREIE UNIVERSITÄT BERLIN   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHMS; ARTIFICIAL INTELLIGENCE; BIOLOGICAL MEMBRANES; FEATURE EXTRACTION; LEARNING SYSTEMS; MOLECULAR STRUCTURE; NEURAL NETWORKS; OPTIMIZATION; PATTERN RECOGNITION; PROTEINS; REFRACTIVE INDEX;

HUMAN INTEGRAL MEMBRANE PROTEINS; HYDROPHOBICITY; MEMBRANE NONMEMBRANE TRANSITION; NEURAL FILTER; PHYSICOCHEMICAL SIDE CHAIN PROPERTIES; TRANSMEMBRANE REGION DETECTION;

AMINO ACIDS;

MEMBRANE PROTEIN;

AMINO ACID SEQUENCE; ARTICLE; FILTER; HUMAN; HYDROPHOBICITY; MEMBRANE STRUCTURE; NERVE CELL NETWORK; STATISTICAL ANALYSIS;

ALGORITHMS; AMINO ACID SEQUENCE; ANTIGENS, CD; ASIALOGLYCOPROTEIN RECEPTOR; CELL ADHESION MOLECULES; DATABASES, FACTUAL; GLYCOPROTEINS; HUMANS; MEMBRANE PROTEINS; MOLECULAR SEQUENCE DATA; NEURAL NETWORKS (COMPUTER); RECEPTORS, CELL SURFACE; RHODOPSIN;

EID: 0030019806     PISSN: 00063525     EISSN: None     Source Type: Journal    
DOI: 10.1002/(sici)1097-0282(199601)38:1<13::aid-bip2>3.0.co;2-z     Document Type: Article

References (55)

1. Schneider, G. & Wrede, P. (1993) J. Mol. Evol. 36, 586-595.
2. Schneider, G. & Wrede, P. (1993) Protein Seq. Data Anal. 5, 419-421.
3. Schneider, G. & Wrede, P. (1994) Biophys. J. 66, 335-344.
4. Qian, N. & Sejnowski, T. J. (1988) J. Mol. Biol. 202, 865-884.
5. Holley, H. L. & Karplus, M. (1991) Methods Enzymol. 210, 610-636.
6. Hirst, J. D. & Sternberg, M. J. E. (1992) Biochemistry 31, 7211-7218.
7. Gasteiger, J. & Zupan, J. (1993) Neural Networks for Chemists - An Introduction, VCH Verlagsgesellschaft, Weinheim, New York.
8. Bremermann, H. J. (1973) in Pattern Recognition in Biological and Technical Systems, Grüsser, O. J. & Klinke, R., Eds., Springer-Verlag, Berlin/Heidelberg, pp. 31-45.
9. Rumelhart, D. E., McClelland, J. L. & The PDP Research Group (Eds.) (1986) Parallel Distributed Processing, Vol. I, MIT Press, Cambridge, MA.
10. Lohmann, R. (1990) in Evolution and Optimization '89, Voigt, H. M., Mühlenbein, H. & Schwefel, H. P., Eds., Akademie-Verlag, Berlin, pp. 61-68.
11. Lohmann, R. (1992) in Dynamic, Genetic, and Chaotic Programming, Souçek, B., & the IRIS Group, Eds., John Wiley & Sons, New York, pp. 395-413.
12. Lohmann, R. (1993) Biol. Cyber. 69, 319-326.
13. Rechenberg, I. (1973) Evolutionsstrategie - Optimierung technischer Systeme nach Prinzipien der biologischen Evolution, Frommann-Holzboog, Stuttgart.
14. Goldberg, D. E. (1989) Genetic Algorithms in Search, Optimization, and Machine Learning, Addison-Wesley, Redwood City, CA.
15. Davidor, Y. & Schwefel, H. P. (1992) in Dynamic, Genetic, and Chaotic Programming, Souçek, B., & the IRIS Group, Eds., John Wiley & Sons, New York, pp. 183-202.
16. Koza, J. R. (1992) Genetic Programming: On the Programming of Computers by Means of Natural Selection, MIT Press, Cambridge, MA.
17. Lohmann, R. (1991) Ph.D. thesis, Technical University Berlin.
18. Lohmann, R. (1991) Wissenschaft. Zeit. TH Ilmenau, 37, 61-65.
19. Kyte, J. & Doolittle, R. F. (1982) J. Mol. Biol. 157, 105-132.
20. Eisenberg, D., Weiss, R. M. & Terwilliger, T. C. (1984) Proc. Natl. Acad Sci. USA 81, 140-144.
21. Finer-Moore, J. & Stroud, R. M. (1984) Proc. Natl. Acad. Sci. USA 81, 155-159.
22. Rose, G. D., Geselowitz, A. R., Lesser, G. J., Lee, R. H. & Zehfus, M. H. (1985) Science 229, 834-838.
23. Klein, P., Kanehisa, M. & DeLisi, C (1985) Biochim. Biophys. Acta 815, 468-476.
24. Vogel, H., Wright, J. K. & Jähnig, F. (1985) EMBO J. 4, 3625-3631.
25. Engelman, D. A., Steitz, T. A. & Goldman, A. (1986) Ann. Rev. Biophys. Biophys. Chem. 15, 321-353.
26. Bangham, J. A. (1988) Anal. Biochem. 174, 142-145.
27. Cronet, P., Sander, C. & Vriend, G. (1993) Protein Eng. 6, 59-64.
28. Taylor, W. R., Jones, D. T. & Green, N. M. (1994) Proteins Struct. Fund. Genet. 18, 281-294.
29. Swiss-Prot Protein Sequence Database (Rel. 20, 1993). EMBL Data Library, D-6900 Heidelberg, FRG and A. Bairoch, Dept. de Biochimie Medicale, Centre Medical Universitaire, 1211 Geneva 4, Switzerland. Distributed by IntelliGenetics Inc., 700 East Camino Real, Mountain View, CA 94040, USA.
30. Boyd, D., Manoil, C. & Beckwith, J. (1987) Proc. Natl. Acad. Sci. USA 84, 8525-8529.
31. von Heijne, G. & Gavel, Y. (1988) Eur. J. Biochem. 174, 671-678.
32. Nielsson, I. & von Heijne, G. (1990) Cell 62, 1135-1141.
33. White, S. A. & Jacobs, R. E. (1990) J. Membrane Biol. 115, 145-158.
34. Schneider, G. & Wrede, P. (1992) Endocytobiosis Cell Res. 9, 1-12.
35. Zamyatnin, A. A. (1972) Prog. Biophys. Mol. Biol. 24, 107-123.
36. Chothia, C. (1975) J. Mol. Biol. 105, 1-14.
37. Hopp, T. P. & Woods, K. R. (1981) Proc. Natl. Acad Sci. USA 78, 3824-3828.
38. Jones, D. D. (1975) J. Theor. Biol. 50, 167-183.
39. Schwefel, H. P. & Männer, R., Eds. (1991) Parallel Problem Solving from Nature I, Springer-Verlag, Berlin/Heidelberg.
40. Schwefel, H.-P. (1977) Numerische Optimierung von Computermodellen mittels der Evolutionsstrategie, Birkhäuserpubl., Basel, Stuttgart.
41. Männer, R. & Manderick, B. (1992) Parallel Problem Solving from Nature II, North-Holland, Amsterdam.
42. Schulz, G. E. & Schirmer, R. H. (1978) Principles of Protein Structure, Springer Verlag Heidelberg.
43. Kuroki, M., Arakawa, F., Matsuo, Y., Oikawa, S., Nakazato, H. & Matsuoka, Y. (1991) Biochem. Biophys. Res. Commun. 176, 578-585.
44. Spiess, M., Schwartz, A. L. & Lodish, H. F. (1985) J. Biol. Chem. 260, 1979-1982.
45. Nathans, J. & Hogness, D. S. (1984) Proc. Natl. Acad. Sci. USA 81, 4851-4855.
46. von Heijne, G. (1985) J. Mol. Biol. 184, 99-105.
47. Esposti, D., Crimi, M. & Venturoli, G. (1990) Eur. J. Biochem. 190, 207-290.
48. Jähnig, F. (1990) Trends Biochem. Sci. 15, 93-95.
49. v. Heijne, G. (1986) EMBO J. 5, 3021-3027.
50. Lohmann, R., Schneider, G., Behrens, D. & Wrede, P. (1994) Protein Sci. 3, 1597-1601.
51. Lohmann, R. (1994) ISCIE Proceedings, Japan-U.S.A., Symposium on Flexible Automation III, Kobe, Japan, pp. 1293-1300.
52. v. Heijne, G. (1989) Nature, 341, 456-458.
53. Dombi, G. & Lawrence, J. (1994) Protein Sci. 3, 557-566.
54. Fasman, G. D. & Gilbert, W. A. (1990) Trends Biochem. Sci. 15, 89-92.
55. Schneider, G., Lohmann, R. & Wrede, P. (1994) in Concepts in Protein Engineering and Design, Wrede, P. & Schneider, G., Eds., Walter de Gruyter, pp. 281-317.