Effective function annotation through catalytic residue conservation

Proceedings of the National Academy of Sciences of the United States of America

Volumn 102, Issue 35, 2005, Pages 12299-12304

  George, Richard A ^a,b   Spriggs, Ruth V ^a,b   Bartlett, Gail J ^b,c   Gutteridge, Alex ^b   MacArthur, Malcolm W ^b   Porter, Craig T ^b   Al Lazikani, Bissan ^a   Thornton, Janet M ^b   Swindells, Mark B ^a  

^a Inpharmatica   (United Kingdom)

^b EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

^c IMPERIAL COLLEGE LONDON   (United Kingdom)

Author keywords

EC; Enzymes; Function prediction; PSI BLAST

Indexed keywords

DEXTRO AMINO ACID; HAPTOGLOBIN; LIGASE; TRYPSIN;

ACCURACY; ARTICLE; ENZYME MECHANISM; GENE SEQUENCE; GENETIC CONSERVATION; GENOME ANALYSIS; GENOMICS; HIGH THROUGHPUT SCREENING; PRIORITY JOURNAL; PROTEOMICS; QUALITY CONTROL; STRUCTURE ANALYSIS;

AMINO ACID SEQUENCE; ANIMALS; CATALYTIC DOMAIN; CONSERVED SEQUENCE; DATABASES, PROTEIN; ENZYMES; GENOMICS; HAPTOGLOBINS; HUMANS; MOLECULAR SEQUENCE DATA; PROTEINS; PROTEOMICS; SEQUENCE HOMOLOGY, AMINO ACID; TRYPSIN;

EID: 24644517567     PISSN: 00278424     EISSN: None     Source Type: Journal    
DOI: 10.1073/pnas.0504833102     Document Type: Article

References (39)

1. Whisstock, J. C. & Lesk, A. M. (2003) Q. Rev. Biophys., 36, 307-340.
2. Altschul, S. F., Madden, T. L., Schaffer, A. A., Zhang, J., Zhang, Z., Miller, W. & Lipman, D. J. (1997) Nucleic Acids Res. 25, 3389-3402.
3. Anonymous (1999) Scientist 13, 15.
4. Jones, D. T. (1999) J. Mol. Biol. 287, 797-815.
5. Todd, A. E., Orengo, C. A. & Thornton, J. M. (2001) J. Mol. Biol. 307, 1113-1143.
6. Tian, W. & Skolnick, J. (2003) J. Mol. Biol. 333, 863-882.
7. Bateman, A., Coin, L., Durbin, R., Finn, R. D., Hollich, V., Griffiths-Jones, S., Khanna, A., Marshall, M., Moxon, S., Sonnhammer, E. L., et al. (2004) Nucleic Acids Res. 32, D138-D141.
8. Marchler-Bauer, A., Anderson, J. B., Cherukuri, P. F., DeWeese-Scott, C., Geer, L. Y., Gwadz, M., He, S., Hurwitz, D. I., Jackson, J. D., Ke, Z., et al. (2005) Nucleic Acids Res. 33, D192-D196.
9. Attwood, T. K., Bradley, P., Flower, D. R., Gaulton, A., Maudling, N., Mitchell, A. L., Moulton, G., Nordle, A., Paine, K., Taylor, P., et al. (2003) Nucleic Acids Res. 31, 400-402.
10. Hulo, N., Sigrist, C. J., Le Saux, V., Langendijk-Genevaux, P. S., Bordoli, L., Gattiker, A., De Castro, E., Bucher, P. & Bairoch, A. (2004) Nucleic Acids Res. 30, 235-238.
11. Lewis, S. E. (2005) Genome Biol. 6, 103.
12. Pal, D. & Eisenberg, D. (2005) Structure 13, 121-130.
13. Altschul, S. F., Boguski, M. S., Gish, W. & Wootton, J. C. (1994) Nat. Genet. 6, 119-129.
14. Boeckmann, B., Bairoch, A., Apweiler, R., Blatter, M. C., Estreicher, A., Gasteiger, E., Martin, M. J., Michoud, K., O'Donovan, C., Phan, I., et al. (2003) Nucleic Acids Res. 31, 365-370.
15. Hegyi, H. & Gerstein, M. (2001) Genome Res. 11, 1632-1640.
16. Fagan, R., Swindells, M. B., Overington, J. & Weir, M. (2001) Trends Biochem. Sci. 26, 213-214.
17. Iyer, L. M., Aravind, L., Bork, P., Hofmann, K., Mushegian, A. R., Zhulin, I. B. & Koonin, E. V. (2001) Genome Biol. 2, RESEARCH0051.1-10.
18. Galperin, M. Y. & Koonin, E. V. (1998) In Silico Biol. 1, 55-67.
19. Livingstone, C. D. & Barton, G. J. (1993) Comput. Appl. Biosci. 9, 745-756.
20. Lichtarge, O., Bourne, H. R. & Cohen, F. E. (1996) J. Mol. Biol. 257, 342-358.
21. Mihalek, I., Res, I. & Lichtarge, O. (2004) J. Mol. Biol. 336, 1265-1282.
22. Porter, C. T., Bartlett, G. J. & Thornton, J. M. (2004) Nucleic Acids Res. 32, D129-D133.
23. Herman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N. & Bourne, P. E. (2000) Nucleic Acids Res. 28, 235-242.
24. International Union of Biochemistry and Molecular Biology (1992) Enzyme Nomenclature: Recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the Nomenclature and Classification of Enzymes (Academic, New York).
25. Jones, D. T. & Swindells, M. B. (2002) Trends Biochem Sci. 27, 161-164.
26. Swindells, M. B., Rae, M., Pearce, M., Moodie, S., Miller, R. & Leach, P. (2002) Philos. Trans. R. Soc. London A 360, 1179-1189.
27. Thompson, J. D., Higgins, D. G. & Gibson, T. J. (1994) Nucleic Acids Res. 22, 4673-4680.
28. Smith, T. F. & Waterman, M. S. (1981) J. Mol. Biol. 147, 195-197.
29. Bairoch, A., Apweiler, R., Wu, C. H., Barker, W. C., Boeckmann, B., Ferro, S., Gasteiger, E., Huang, H., Lopez, R., Magrane, M., et al. (2005) Nucleic Acids Res. 33, D154-D159.
30. Fan, C., Moews, P. C., Walsh, C. T. & Knox, J. R. (1994) Science 266, 439-443.
31. Galperin, M. Y. & Koonin, E. V. (1997) Protein Sci. 6, 2639-2643.
32. Li, H., Xu, H., Graham, D. E. & White, R. H. (2003) Proc. Natl. Acad. Sci. USA 100, 9785-9790.
33. Schroder, H. K., Willassen, N. P. & Smalas, A. O. (1998) Acta Crystallogr. D 54, 780-798.
34. Sanishvili, R., Yakunin, A. F., Laskowski, R. A., Skarina, T., Evdokimova, E., Doherty-Kirby, A., Lajoie, G. A., Thornton, J. M., Arrowsmith, C. H., Savchenko, A., et al. (2003) J. Biol. Chem. 278, 26039-26045.
35. Hubbard, T., Andrews, D., Caccamo, M., Cameron, G., Chen, Y., Clamp, M., Clarke, L., Coates, G., Cox, T., Cunningham, F., et al. (2005) Nucleic Acids Res. 33, D447-D453.
36. Benson, D. A., Karsch-Mizrachi, I., Lipman, D. J., Ostell, J. & Wheeler, D. L. (2005) Nucleic Acids Res. 33, D34-D38.
37. Kanz, C., Aldebert, P., Althorpe, N., Baker, W., Baldwin, A., Bates, K., Browne, P., van den Broek, A., Castro, M., Cochrane, G., et al. (2005) Nucleic Acids Res. 33, D29-D33.
38. Tateno, Y., Saitou, N., Okubo, K., Sugawara, H. & Gojobori, T. (2005) Nucleic Acids Res. 33, D25-D28.
39. Lesk, A. M. & Chothia, C. (1988) Nature 335, 188-190.