Novel method to detect a motif of local structures in different protein conformations

Protein Engineering

Volumn 11, Issue 11, 1998, Pages 981-990

  Wako, Hiroshi ^a   Yamato, Takahisa ^b  

^a WASEDA UNIVERSITY   (Japan)

^b NAGOYA UNIVERSITY   (Japan)

Author keywords

Delaunay tessellation; Residue residue interaction; Structural classification; Structural codes; Structural motifs

Indexed keywords

PROTEIN;

ARTICLE; DATA BASE; PRIORITY JOURNAL; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE;

EID: 0031736346     PISSN: 02692139     EISSN: None     Source Type: Journal    
DOI: 10.1093/protein/11.11.981     Document Type: Article

References (37)

1. Alexandrov, N.N. and Go, N. (1994) Protein Sci., 3, 866-875.
2. Alexandrov, N.N., Takahashi, K. and Go, N. (1992) J. MoI. Biol, 225, 5-9.
3. Aurora, R., Srinivasan, R. and Rose, G.D. (1994) Science, 264, 1126-1130.
4. Barber, C.B., Dobkin, D.P. and Huhdanpaa, H.T. (1995) ACM: Trans on Mathematical Software, 22, 469-483.
5. Chan, A.W.E., Hutchinson, E.G., Harris, D. and Thornton, J.M. (1993) Protein Sci., 2, 1574-1590.
6. Chelvanayagam, G., Roy, G. and Argos, P. (1994) Protein Engng, 7, 173-184.
7. Chothia, C. and Lesk, A.M. (1986) EMBO J., 5, 823-826.
8. Flores, T.P., Orengo, C.A., Moss, D.S. and Thornton, J.M. (1993) Protein Sci., 2, 1811-1826.
9. Go, M. (1995) Adv. Biophys, 19, 91-131.
10. Harper, E.T. and Rose, G.D. (1993) Biochemistry, 32, 7605-7609.
11. Holm, L. and Sander, C. (1993) J. MoI. Biol., 233, 123-138.
12. Holm, L. and Sander, C. (1994) Nucleic Acids Res., 22, 3600-3609.
13. Holm, L. and Sander, C. (1996) Methods Enzymol., 266, 653-662.
14. Hutchinson, E.G. and Thornton, J.M. (1996) Protein Sci., 5, 212-220.
15. Johnson, M., Sutcliffe, M. and Blundell, T.L. (1990a) J. Mol. Evol., 30, 43-59.
16. Johnson, M., Sali, A. and Blundell, T.L. (1990b) Methods Ezymol., 183, 670-690.
17. Kline, T.P., Brown, K., Brown, S.C., Jeffs, P.W., Kopple, K.D. and Mueller, L. (1990) Biochemistry, 29, 7805-7813.
18. Kobayashi, N., Yamato, T. and Go, N. (1997) Proteins Struct. Funct. Genet., 28, 109-116.
19. Kraulis, P.J. (1991) J. Appl. Crystallogr., 24, 946-950.
20. Kretsinger, R.H. (1980) Crit. Rev. Biochem., 8, 119-174.
21. Mizuguchi, K. and Go, N. (1995) Protein Engng, 8, 353-362.
22. Munson, P.J. and Singh, R.K. (1997) Protein Sci., 6, 1467-1481.
23. Murzin, A.G., Brenner, S.E., Hubbard, T. and Chothia, T. (1995) J. Mol. Biol., 247, 536-540.
24. Orengo, C.A., Flores, T.P., Taylor, W.R. and Thornton, J.M. (1993) Protein Engng, 6, 485-500.
25. Orengo, C.A., Mitchie, A., Jones, S., Jones, D., Swindells, M. and Thornton, J. (1996) PDB Quarterly Newsletter, 78, 8-9.
26. Orengo, C.A. and Taylor, W.R. (1996) Methods Enzymol., 266, 617-635.
27. Richardson, J.S. (1981) Adv. Protein Chem., 34, 167-339.
28. Russell, R. and Barton, G. (1994) J. Mol. Biol., 244, 332-350.
29. Sali, A. and Blundell, T.L. (1990) J. Mol. Biol., 212, 403-428.
30. Sander, C. and Schneider, R. (1991) Proteins Struct. Funct. Genet., 9, 56-68.
31. Schulz, G.E. and Schirmer, R.H. (1979) Principles of Protein Structure, Springer-Verlag, Berlin.
32. Singh, R.K., Tropsha, A. and Vaisman, I. (1996) J. Comp. Biol., 3, 213-221.
33. Taylor, W.R. and Orengo, C.A. (1989) J. Mol. Biol., 208, 1-22.
34. Vaisman, I.I., Brown, F.K. and Tropsha, A. (1994) J. Phys. Chem., 89, 5559-5564.
35. Voloshin, V.P., Naberukhin, Y.I. and Medvedev, N.N. (1989) Mol. Simulation, 4, 209-227.
36. Yamato, T. (1996) J. Mol. Graph., 14, 105-107.
37. Yamato, T., Saito, M. and Higo, J. (1994) Chem. Phys. Lett., 219, 155-159.