Identifying nature's protein lego set

Advances in Protein Chemistry

Volumn 54, Issue , 2000, Pages 159-183

  Das, Sudeshna ^a   Smith, Temple F ^b  

^a MILLENNIUM PHARMACEUTICALS INC   (United States)

^b Boston University   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

PRIORITY JOURNAL; PROTEIN DOMAIN; REVIEW; SEQUENCE ANALYSIS; SEQUENCE HOMOLOGY;

EID: 0033909565     PISSN: 00653233     EISSN: None     Source Type: Book Series    
DOI: 10.1016/s0065-3233(00)54006-6     Document Type: Review

References (60)

1. Adams, R. M., Das, S., and Smith, T. F. (1996). Protein Sci. 5, 1240-1249.
2. Altschul, S. F., Gish, W., Miller, W., Myers, E. W., and Lipman, D. J. (1990). J. Mol. Biol. 215, 403-410.
3. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W., and Lipman, D. J. (1997). Nucleic Acids Res. 25(17), 3389-3402.
4. Arratia, R., and Waterman, M. (1985). Adv. Math. 55, 13-23.
5. Bairoch, A. (1992). Nucleic Acids Res. 20, 2013-2018.
6. Bairoch, A. (1994). Nucleic Acids Res. 22, 3626-3627.
7. Bairoch, A., and Boeckmann, B. (1994). Nucleic Acids Res. 22, 3578-3580.
8. Baron, M., Norman, D. G., and Campbell, I. D. (1991). TIBS 16, 13-17.
9. Barrett, C., Hughey, R., and Karplus, K. (1997). CABIOS 13(2), 191-199.
10. Barton, G. J., and Sternberg, M. J. E. (1987). J. Mol. Biol. 198, 327-337.
11. Barton, G. J., and Sternberg, M. J. E. (1990). J. Mol. Biol. 212, 389-402.
12. Bernstein, F., Koetzle, T., Williams, G., Meyer, E., Brice, M., Rodgers, J., Kennard, O., Schimanouchi, T., and Tasumi, M. (1977). J. Mol. Biol. 112, 535-542.
13. Brown, M., Hughey, R., Krogh, A., Mian, I., Sjölander, K., and Haussler, D. (1993). ISMB 93, 47-55.
14. Carrillo, H., and Lipman, D. (1988). SIAM J. Appl. Math. 48, 1073-1082.
15. Chomsky, N. (1957). "Syntactic Structures." Mouton, The Hague.
16. Claverie, J. (1994). Comput. Chem. 18, 287-293.
17. Claverie, J.-M. (1995). In "Advances in Computational Biology" (H. Villar, ed.), JAI Press, London.
18. Dayhoff, M. O., and Eck, R. V. (1966). "Atlas of Protein Sequence and Structure." Vol. 2, NBRF Press, Silver Spring, MD.
19. Dayhoff, M. O., Schwartz, R. M., and Orcutt, B. (1978). "Atlas of Protein Sequence and Structure" Vol. 5, 345-358.
20. Feng, D. F., and Doolittle, R. F. (1987). J. Mol. Evol. 25, 351-360.
21. Friedman, P., and Przysiecki, C. (1987). Int. J. Biochem. 19, 1-7.
22. Goldstein, L., and Waterman, M. (1994). J. Comput. Biol. 1, 93-104.
23. Gribskov, M., and Burgess, R. (1986). Nucleic Acids Res. 14, 6745-6763.
24. Gribskov, M., McLachlan, A. D., and Eisenberg, D. (1987). Proc. Natl. Acad. Sci. USA 84(13), 4355-4358.
25. Henikoff, J. G., and Henikoff, S. (1996). CABIOS 12(2), 135-143.
26. Henikoff, S., and Henikoff, J. G. (1991). Nucl. Acid. Res. 19(23), 6565-6572.
27. Henikoff, S., and Henikoff, J. G. (1992). Proc. Natl. Acad. Sci. USA 89, 10915-10919.
28. Hertz, G. Z., and Stormo, G. D. (1990). CABIOS 6, 81-92.
29. Higgins, D. J., Thompson, J. D., and Gibson, T. J. (1996). Methods Enzymol. 266, 383-400.
30. Holm, L., and Sander, C. (1997). Nucleic Acids Res. 25, 231-234.
31. Johnson, M. S., and Doolittle, R. F. (1986). J. Mol. Evol. 23, 267-278.
32. Karlin, S., and Altschul, S. F. (1990). Proc. Natl. Acad. Sci. USA 87, 2264-2268.
33. Kendrew, J. C. (1958). Nature 181, 662-666.
34. Krogh, A., Brown, M., Mian, I. S., Sjölander, K., and Haussler, D. (1994). J. Mol. Biol. 235, 1501-1531.
35. Lawrence, C. E., Altschul, S. F., Boguski, M. S., Liu, J. S., Neuwald, A. F., and Wooton, J. C. (1993). Science 262, 208-214.
36. Livingstone, G. D., and Barton, G. J. (1993). CABIOS 9, 745-756.
37. Lonetto, M., Gribskov, M., and Gross, C. (1992). J. Bacteriol. 174, 3843-3849.
38. Needleman, S. B., and Wunsch, C. D. (1970). J. Mol. Biol. 48, 443-453.
39. Pearson, W. R., and Lipman, D. J. (1988). Proc. Natl. Acad. Sci. USA 85, 2444-2448.
40. Richardson, J. (1981). Adv. Protein Chem. 34, 167-339.
41. Schulz, G. E., and Schirmer, R. H. (1979). "Principles of Protein Structure." Springer-Verlag, New York.
42. Sjölander, K., Karplus, K., Brown, M., Highey, R., Krogh, A., Mian, I., and Haussler, D. (1996). CABIOS 12, 327-345.
43. Smith, R. F., and Smith, T. F. (1990). Proc. Natl. Acad. Sci. USA 87, 118-122.
44. Smith, R. F., and Smith, T. F. (1992). Protein Eng. 5(1), 35-41.
45. Smith, T., Lathrop, R., and Cohen, F. (1996). In "Integrative Approaches to Molecular Biology" (J. Collado-Vides, B. Magasanik, and T. F. Smith, eds.), MIT Press, Cambridge, MA, 29-61.
46. Smith, T., Waterman, M., and Burks, C. (1985). Nucleic Acids Res. 13, 645-656.
47. Smith, T. F. (1998). Trends Genet. 14(7), 291-293.
48. Smith, T. F., and Waterman, M. S. (1981). J. Mol. Biol. 147, 195-197.
49. Smith, T. F., and Zhang, X. (1997). Nat. Biotechnol. 15, 1222-1223.
50. Sneath, P. H., and Sokal, R. R. (1973). "Numerical Taxonomy." Freeman, San Francisco.
51. Sonnhammer, E., Eddy, S., and Durbin, R. (1997). Proteins 28(3), 405-420.
52. Stormo, G. D., Schneider, T. D., Gold, L., and Ehrenfeucht, A. (1982). Nucleic Acids Res. 10, 2997-3011.
53. Tatusov, R., Altschul, S., and Koonin, E. (1994). Proc. Natl. Acad. Sci. USA 91, 12091-12095.
54. Taylor, W. (1987). CABIOS 3, 81-87.
55. Thompson, J. D., Higgins, D. G., and Gibson, T. J. (1994). CABIOS 10, 19-29.
56. Vermeer, C. (1990). Biochem. J. 266, 625-636.
57. Wallace, J. C., and Henikoff, S. (1992). CABIOS 8, 249-254.
58. Waterman, M., and Perlwitz, M. (1986). Bull. Math. Biol. 46, 567-577.
59. Waterman, M. S., Smith, T. F., and Beyer, W. A. (1976). Adv. Math. 20(3), 367-387.
60. Zuckerkandl, E., and Pauling, L. C. (1965). J. Theor. Biol. 8, 357-358.