Combining sensitive database searches with multiple intermediates to detect distant homologues

Protein Engineering

Volumn 12, Issue 2, 1999, Pages 95-100

  Salamov, Asaf A ^a,b   Suwa, Makiko ^a   Orengo, Christine A ^c   Swindells, Mark B ^a,d,e  

^a Helix Research Institute   (Japan)

^b WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

^c UNIVERSITY COLLEGE LONDON   (United Kingdom)

^d UNIVERSITY OF TSUKUBA   (Japan)

^e Inpharmatica Ltd   (United Kingdom)

Author keywords

CATH; Intermediate searches; Protein structure; Sequence analysis

Indexed keywords

PROTEIN;

ALGORITHM; ARTICLE; DATA BASE; PRIORITY JOURNAL; PROTEIN STRUCTURE; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY; TECHNIQUE;

EID: 0032940341     PISSN: 02692139     EISSN: None     Source Type: Journal    
DOI: 10.1093/protein/12.2.95     Document Type: Article

References (29)

1. Abagyan, R. and Batalov, S. (1997) J. Mol. Bio., 273, 355-368.
2. Altschul, S.F. and Gish, W. (1996) Methods Enzymol., 266, 460-480.
3. Altschul, S.F., Gish, W., Miller, W., Myers, E.W. and Lipman, D.J. (1990) J. Mol. Biol., 215, 403-410.
4. 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.
5. Bernstein, F.C., Koetzle, T.F., Williams, G.J.B., Meyer, E.F.,Jr. Brice, M.D., Rodgers, J.R., Kennard, O., Shimanouchi, T. and Tusumi, M. (1977) J. Mol. Biol., 122, 535-542.
6. Bork, P., Gellerich, J., Groth, H., Hooft, R. and Martin, F. (1995) Protein Sci., 4, 268-274.
7. Dayhoff, M.O., Schwartz, R.M. and Orcutt, B.C. (1978) In Dayhoff, M.O. (ed.), Atlas of Protein Sequence and Structure, Vol. 5, National Biomedical Research Foundation, Washington, DC, pp. 345-352.
8. Feng, D.F., Johnson, M.S. and Doolittle, R.F. (1985) J. Mol. Evol., 21, 112-125.
9. Gonnet, G.H., Cohen, M.A. and Benner, S.A. (1992) Science, 256, 1443-1445.
10. Gotoh, O. (1982) J. Mol. Biol., 162, 705-708.
11. Gribskov, M. (1992) Gene. 119, 107-111.
12. Henikoff, S. and Henikoff, J.G. (1992) Proc. Natl Acad. Sci. USA, 89, 10915-10919.
13. Holm, L. and Sander, C. (1997) Proteins. 28, 72-82.
14. Johnson, M.S. and Overington, J.P. (1993) J. Mol. Biol., 233, 716-738.
15. Jones, D.T., Taylor, W.R. and Thornton, J.M. (1992) Comput. Appl. Biosci., 8, 275-282.
16. Karlin, S. and Altschul, S.F. (1990) Proc. Natl Acad. Sci. USA, 87, 2264-2268.
17. Koonin, E. and Tatsuov, R.L. (1994) J. Mol. Biol., 244, 125-132.
18. McLachlan, A.D. (1971) J. Mol. Biol., 61, 409.
19. Mott, R. (1991) Bull. Math. Biol., 54, 59-75.
20. Needleman, S.B. and Wunsch, C.D. (1970) J. Mol. Biol., 48, 443-453.
21. Orengo, C.A., Michie, A.D., Jones, S., Jones, D.T., Swindells, M.B. and Thornton, J.M. (1997) Structure, 5, 1093-1108.
22. Park, J., Teichmann, S.A., Hubbard, T. and Chothia, C. (1997) J. Mol. Biol., 273, 349-354.
23. Pearson, W.R. (1995) Protein Sci., 4, 1145-1160.
24. Pearson, W.R. (1996) Methods Enzymol., 266, 227-258.
25. Pearson, W.R. and Lipman, D.J. (1988) Proc. Natl Acad. Sci. USA, 85, 2444-2448.
26. Sander, C. and Schneider, R. (1991) Proteins. 9, 56-68.
27. Smith, T.F. and Waterman, M.S. (1981) J. Mol. Biol., 147, 195-197.
28. Sonnhammer, E.L.L., Eddy, S.R., Birhey, E., Bateman, A. and Durbin, R. (1998) Nucleic Acids Res., 26, 322-325.
29. Sphaer, E.G., Robinson, M., Yee, D., Candlin, J.D., Mines, R. and Hunkapiller, T. (1996) Genomics, 38, 179-191.