Protein sequence alignment techniques

Acta Crystallographica Section D: Biological Crystallography

Volumn 54, Issue 6 I, 1998, Pages 1139-1146

  Barton, Geoffrey J ^a  

^a WELLCOME TRUST SANGER INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

AMINO ACID SEQUENCE; PROTEIN SEQUENCE ALIGNMENT;

ALGORITHMS; PROTEIN CONFORMATION; SEQUENCE ALIGNMENT;

EID: 0032214046     PISSN: 09074449     EISSN: None     Source Type: Journal    
DOI: 10.1107/S0907444998008324     Document Type: Conference Paper

References (44)

1. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. (1990). J. Mol. Biol. 215, 403-410.
2. Barton, G. J. (1990). Methods Enzymol. 183, 403-428.
3. Barton, G. J. (1993a). Comput. Appl. Biosci. 9, 729-734.
4. Barton, G. J. (1993b). Protein Eng. 6, 37-40.
5. Barton, G. J. & Sternberg, M. J. E. (1987a). Protein Eng. 1, 89-94.
6. Barton, G. J. & Sternberg, M. J. E. (1987b). J. Mol. Biol. 198, 327-337.
7. Barton, G. J. & Sternberg, M. J. E. (1990). J. Mol. Biol. 212, 389-402.
8. Bucher, P., Karplus, K., Moeri, N. & Hofmann, K. (1996). Comput. Chem. 20(1), 3-23.
9. Dayhoff, M. O., Schwartz, R. M. & Orcutt, B. C. (1978). A Model of Evolutionary Change in Proteins. Matrices for Detecting Distant Relationships. In Atlas of Protein Sequence and Structure. Vol. 5, edited by M. O. Dayhoff, pp. 345-358. Washington DC: National Biomedical Research Foundation.
10. Gibbs, A. J. & McIntyre, G. A. (1970). Eur. J. Biochem. 16, 1-11.
11. Gotoh, O. (1982). J. Mol. Biol. 162, 705-708.
12. Gotoh, O. (1996). J. Mol. Biol. 264(4), 823-838.
13. Gribskov, M., McLachlan, A. D. & Eisenberg, D. (1987). Proc. Natl Acad. Sci. USA, 84, 4355-4358.
14. Gusfield, D. (1997). Algorithms on Strings, Trees, and Sequences: Computer Science and Computational Biology. Cambridge University Press.
15. Henikoff, S. & Henikoff, J. G. (1992). Proc. Natl Acad. Sci. USA, 89, 10915-10919.
16. Henikoff, S. & Henikoff, J. G. (1993). Proteins Struct. Funct. Genet. 17, 49-61.
17. Jones, D. T., Taylor, W. R. & Thornton, J. M. (1992). Comput. Appl. Biosci. 8, 275-82.
18. Krogh, A., Brown, M., Mian, I. S., Sjolander, K. & Haussler, D. (1994). J. Mol. Biol. 235, 1501-1531.
19. Lesk, A. M., Levitt, M. & Chothia, C. (1986). Protein Eng. 1, 77-78.
20. Lipman, D. J., Altschul, S. F. & Kececioglu, J. (1989). Proc. Natl Acad. Sci. USA, 86, 4412-4415.
21. Livingstone, C. D. & Barton, G. J. (1993). Comput. Appl. Biosci. 9, 745-756.
22. Livingstone, C. D. & Barton, G. J. (1996). Methods Enzymol. 266, 497-512.
23. Murata, M., Richardson, J. S. & Sussman, J. L. (1985). Proc. Natl Acad. Sci. USA, 82, 3073-3077.
24. Myers, E. W. & Miller, W. (1988). Comput. Appl. Biosci. 4, 11-17.
25. Needleman, S. B. & Wunsch, C. D. (1970). J. Mol. Biol. 48, 443-453.
26. Notredame, C. & Higgins, D. G. (1996). Nucleic Acid. Res. 24(8), 1515-1524.
27. Overington, J., Donnelly, D., Johnson, M. S., Sali, A. & Blundell, T. L. (1992). Protein Sci. 1, 216-226.
28. Pascarella, S. & Argos, P. (1992). J. Mol. Biol. 224, 461-471.
29. Raghava, G. P. S. & Barton, G. J. (1998). Protein Sci. Submitted.
30. Russell, R. B. & Barton, G. J. (1992). Proteins Struct. Funct. Genet. 14, 309-323.
31. Sankoff, D. & Kruskal, J. B. (1983). Editors. Time Warps, String Edits unit Macromolecules: the Theory and Practice of Sequence Comparison. New York: Addison Wesley.
32. Saqi, M. A. S. & Sternberg, M. J. E. (1991). J. Mol. Biol. 219, 727-732.
33. Sellers, P. H. (1974). SIAM J. Appl. Math. 26, 787-793.
34. Smith, T. F. & Waterman, M. S. (1981). J. Mol. Biol. 147, 195-197.
35. Sonnhammer, E. L. L. & Durbin, R. (1995). Gene-Combis. 167, 1-10.
36. Staden, R. (1982). Nucleic Acid. Res. 10(9), 2951-2961.
37. Taylor, W. R. (1986a). J. Theor. Biol. 119, 205-218.
38. Taylor, W. R. (1986b). J. Mol. Biol. 188, 233-258.
39. Thompson, J. D., Higgins, D. G. & Gibson, T. J. (1994). Nucleic Acid. Res. 22, 4673-4680.
40. Vingron, M. & Argos, P. (1990). Protein Eng. 3, 565-569.
41. Vogt, G., Etzold, T. & Argos, P. (1995). J. Mol. Biol. 249, 816-831.
42. Waterman, M. S. & Eggert, M. (1987). J. Mol. Biol. 197, 723-728.
43. Waterman, M. S., Smith, T. F. & Beyer, W. A. (1976). Adv. Math. 20, 367-387.
44. Zuker, M. (1991). J. Mol. Biol. 221, 403-420.