Assessment of pseudo-energy potentials by the best-five test: A new use of the three-dimensional profiles of proteins

Protein Engineering

Volumn 10, Issue 4, 1997, Pages 339-351

  Ota, Motonori ^a,b   Nishikawa, Ken ^a  

^a NATIONAL INSTITUTE OF GENETICS   (Japan)

^b WASEDA UNIVERSITY   (Japan)

Author keywords

3D 1D compatibility function; Denatured state; Fold recognition; Sequence design; Threading

Indexed keywords

AMINO ACID SEQUENCE; ARTICLE; DATA BASE; ELECTRIC POTENTIAL; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; RECOGNITION;

EID: 0030904226     PISSN: 02692139     EISSN: None     Source Type: Journal    
DOI: 10.1093/protein/10.4.339     Document Type: Article

References (37)

1. Abrahams, J.P., Leslie, A.G.W., Lutter, R. and Walker, J.E. (1994) Nature, 370, 621-628.
2. Amano, T., Yoshida, M., Matsuo, Y. and Nishikawa, K. (1994) FEBS Lett., 351, 1-5.
3. Bauer, A. and Beyer, A. (1994) Proteins, 18, 254-261.
4. Bowie, J.U. and Eisenberg, D. (1994) Proc. Natl Acad. Sci. USA, 91, 4436-4440.
5. Bowie, J.U., Clarke, N.D., Pabo, C.O. and Sauer, T. (1990) Proteins, 7, 257-264.
6. Bowie, J.U., Lüthy, R. and Eisenberg, D. (1991) Science, 253, 164-170.
7. Bryant, S.H. and Altschul, S.F. (1995) Curr. Opin. Struct. Biol., 5, 236-244.
8. Bryant, S.H. and Lawrence, C.E. (1993) Proteins, 16, 92-112.
9. Godzik, A (1995) Protein Engng, 8, 409-416.
10. Godzik, A. and Skolnick, J. (1992) Proc. Natl Acad. Sci. USA, 89, 12098-12102.
11. Godzik, A., Skolnick, J. and Kolinski, A. (1992) J. Mol. Biol., 227, 227-238.
12. Godzik, A., Kolinski, A. and Skolnick, J. (1995) Protein Sci., 4, 2107-2117.
13. Goldstein, R.A., Luthey-Schlten, Z.A. and Wolynes, P.G. (1992) Proc. Natl Acad. Sci. USA, 89, 9029-9033.
14. Hendlich, M., Lackner, P., Weitckus, S., Floeckner, H., Froschauer, R., Gottsbacher, K., Casari, G. and Sippl, M. J. (1990) J. Mol. Biol., 216, 167-180.
15. Holm, L., Ouzounis, C., Sander, C., Tuparev, G. and Vriend, G. (1992) Protein Sci., 1, 1691-1698.
16. Jones, D.T., Taylor, W.R. and Thornton, J.M. (1992) Nature, 358, 86-89.
17. Kabsch, W. and Sander, C. (1983) Biopolymers, 22, 2577-2637.
18. Kocher, J.A., Rooman, M.J. and Wodak, S.J. (1994) J. Mol. Biol., 235, 1598-1613.
19. Lüthy, R., Bowie, J.U. and Eisenberg, D. (1992) Nature, 356, 83-85.
20. Maiorov, V.N. and Crippen, G.M. (1992) J. Mol. Biol., 227, 876-888.
21. Maiorov, V.N. and Crippen, G.M. (1994) Proteins, 20, 167-173.
22. Matsuo, Y. and Nishikawa, K. (1994a) FEBS Lett., 345, 23-26.
23. Matsuo, Y. and Nishikawa, K. (1994b) Protein Sci., 3, 2055-2063.
24. Matsuo, Y., Nakamura, H. and Nishikawa, K. (1995) J. Biochem., 118, 137-148.
25. Nishikawa, K. and Matsuo, Y. (1993) Protein Engng, 6, 811-820.
26. Ota, M. (1996) Ph.D. thesis, Waseda University, 1996.
27. Ota, M., Kanaya, S. and Nishikawa, K. (1995) J. Mol. Biol., 248, 733-738.
28. Ouzounis, C., Sander, C., Scharf, M. and Schneider, R.J. (1993) J. Mol. Biol., 232, 805-825.
29. Rooman, M.J. and Wodak, S.J. (1995) Protein Engng, 8, 849-858.
30. Russell, R.B. and Barton, G.J. (1994) J. Mol. Biol., 244, 332-350.
31. Sasai, M. (1995) Proc. Natl Acad. Sci. USA, 92, 8438-8442.
32. Singh, J. and Thornton, J.M. (1990) J. Mol. Biol., 211, 595-615.
33. Sippl, M.J. (1990) J. Mol. Biol., 213, 859-883.
34. Sippl, M.J. (1993) Proteins, 17, 355-362.
35. Sugiyama, S., Vassylyev, D.G., Matsushima, M., Kashiwagi, K., Igarashi, K. and Morikawa, K. (1996) J. Biol. Chem., 271, 9519-9525.
36. Wilmanns, M. and Eisenberg, D. (1993) Proc. Natl Acad. Sci. USA, 90, 1379-1383.
37. Wodak, S.J. and Rooman, M.J. (1993) Curr. Opin. Struct. Biol., 3, 247-259.