Recognition of analogous and homologous protein folds - Assessment of prediction success and associated alignment accuracy using empirical substitution matrices

Protein Engineering

Volumn 11, Issue 1, 1998, Pages 1-9

  Russell, Robert B ^a,b   Saqi, Mansoor A S ^b   Bates, Paul A ^a   Sayle, Roger A ^b   Sternberg, Michael J E ^a  

^a IMPERIAL CANCER RESEARCH FUND   (United Kingdom)

^b GLAXOSMITHKLINE   (United Kingdom)

Author keywords

Evolution; Protein folding; Protein prediction; Threading

Indexed keywords

ALGORITHM; ARTICLE; EVOLUTION; PREDICTION; PRIORITY JOURNAL; PROTEIN FOLDING; PROTEIN SECONDARY STRUCTURE; TECHNIQUE;

EID: 0031909873     PISSN: 02692139     EISSN: None     Source Type: Journal    
DOI: 10.1093/protein/11.1.1     Document Type: Article

References (51)

1. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) J. Mol. Biol., 215, 403-410.
2. Barton, G.J. and Sternberg, M.J.E. (1990) J. Mol. Biol., 212, 389-402.
3. Bates, P.A., Jackson, R.M. and Sternberg, M.J.E. (1996) In Browne, M.J. and Thurlby, P.L. (ed.), Genomes, Molecular Biology and Drug Discovery, Academic Press, London, pp. 73-88.
4. Bernstein, F.C., Koetzle, T.F., Williams, G., Meyer, D.J., Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T. and Tasumi, M. (1977) J. Mol. Biol., 112, 535-542.
5. Birney, E., Thompson, J.D. and Gibson, T.J. (1996) Nucleic Acids Res, 24, 2730-2739.
6. Bowie, J.U., Lüthy, R. and Eisenberg, D. (1991) Science, 253, 164-170.
7. Bryant, S.H. and Lawrence, C.E. (1993) Proteins, 16, 92-112.
8. Dayhoff, M.O., Schwartz, R.M. and Orcutt, B.C. (1978) In Dayhoff, M.O. (ed.) Atlas of Protein Sequence and Structure, National Biomedical Research Foundation, Silver Spring, MD. Vol. 5, pp. 345-358.
9. Defay, T.R. and Cohen, F.E. (1996). J. Mol. Biol., 262, 314-323.
10. Eddy, S.R. (1996) Curr. Opin. Struct. Biol., 6, 361-365.
11. Feng, Z.K. and Sippl, M.J. (1996) Folding Design, 1, 123-132.
12. Fischer, D. and Eisenberg, D. (1996) Protein Sci., 5, 947-955.
13. Godzik, A., Kolinski, A. and Skolnick, J. (1992) J. Mol. Biol., 227, 227-238.
14. Godzik, A. (1996) Protein Sci., 5, 1325-1338.
15. Gonnet, G.H., Cohen, M.A. and Benner, S.A. (1992) Science, 256, 1443-1444.
16. Gribskov, M., McLachlan, A.D. and Eisenberg, D. (1987) Proc. Natl Acad. Sci. USA, 84, 4355-4358.
17. Henikoff, S. and Henikoff, J.G. (1992) Proc. Natl Acad. Sci. USA, 89, 10915-10919.
18. Johnson, M.S., Overington, J.P. and Blundell, T.L. (1993). J. Mol. Biol., 231, 735-752.
19. Jones, D.T. (1997) Curr. Opin. Struct. Biol., 7, 377-387.
20. Jones, D.T., Miller, R.T. and Thornton, J.M. (1995) Proteins, 23, 387-397.
21. Jones, D.T., Taylor, W.R. and Thornton, J.M. (1992) Nature, 358, 86-89.
22. Kabsch, W. and Sander, C. (1983) Biopolymers, 22, 2577-2637.
23. Krogh, A., Brown, M., Mian, I.S., Sjolander, K. and Haussler, D. (1994) J. Mol. Biol., 235, 1501-1531.
24. Lemer, C.M.-R., Rooman, J. and Wodak, S.J. (1995) Proteins, 23, 337-355.
25. Levitt, M. (1997) Proteins, in press.
26. Murzin, A.G. (1993a) J. Mol. Biol., 18, 403-405.
27. Murzin, A.G. (1993b) J. Mol. Biol., 230, 689-694.
28. Murzin, A.G., Brenner, S.E., Hubbard, T. and Chothia, C. (1995) J. Mol. Biol., 247, 536-540.
29. Murzin, A.G., Lesk, A.M. and Chothia, C. (1992) J. Mol. Biol., 223, 531-543.
30. Needleman, S.B. and Wunsch, C.D. (1970) J Mol. Biol., 48, 443-453.
31. Orengo, C.A., Flores, T.P., Taylor, W.R. and Thornton, J.M. (1993) Prot. Engng, 6, 485-500.
32. Orengo, C.A., Jones, D.T. and Thornton, J.M. (1994) Nature, 372, 631-634.
33. Rice, D.W. and Eisenberg, D. (1997) J. Mol. Biol., 267, 1026-1038.
34. Rossmann, M.G. and Argos, P. (1976) J. Mol. Biol., 105, 75-95.
35. Rost, B. (1995) In Rawlings, Clark, D., Altman, R., Hunter, L., Lengauer, T. and Wodak, S. (ed.) The Third International Conference On Intelligent Systems for Molecular Biology (ISMB), Cambridge, UK, Jul 16-19, 1995, AAAI Press, Menlo Park, CA, pp. 314-321.
36. Rost, B. and Sander, C. (1993a) Proc. Natl Acad. Sci. USA, 90, 7558-7562.
37. Rost, B. and Sander, C. (1993b) J. Mol. Biol., 232, 584-599.
38. Rost, B. and Sander, C. (1994) Proteins, 20, 216-226.
39. Rost, B., Schneider, R. and Sander, C. (1997) J. Mol. Biol., 270, 471-480.
40. Russell, R.B. and Barton, G.J. (1992) Proteins, 14, 309-323.
41. Russell, R.B., Copley, R.R. and Barton, G.J. (1996) J. Mol. Biol., 259, 349-365.
42. Russell, R.B., Saqi, M.A., Sayle, R.A., Bates, P.A. and Sternberg, M.J.E. (1997) J. Mol. Biol., 269, 423-439.
43. Sander, C. and Schneider, R. (1991) Proteins, 9, 56-68.
44. Sankoff, D. and Kruskal, J.B. (1983) Time Warps, String Edits and Macromolecules: The Theory and Practice of Sequence Comparison. Addison-Wesley Publishing Co. Inc.
45. Saqi, M.A.S. and Sternberg, M.J.E. (1991) J. Mol. Biol., 219, 727-732.
46. Sali, A. and Blundell, T.L. (1990) J. Mol. Biol., 212, 403-428.
47. Sippl, M.J. (1990) Mol. Biol., 213, 859-883.
48. Sippl, M.J. and Weitckus, S. (1992) Proteins, 13, 258-271.
49. Taylor, W.R. (1997) J. Mol. Biol., 269, 902-943.
50. Taylor, W.R. and Orengo, C.A. (1989) J. Mol. Biol., 208, 1-22.
51. Torda, A.E. (1997) Curr. Opin. Struct. Biol., 7, 200-205.