Secondary-structure matching (SSM), a new tool for fast protein structure alignment in three dimensions

Acta Crystallographica Section D: Biological Crystallography

Volumn 60, Issue 12 I, 2004, Pages 2256-2268

  Krissinel, E ^a   Henrick, K ^a  

^a EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN;

ALGORITHM; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; INTERNET; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE; QUALITY CONTROL;

ALGORITHMS; INTERNET; MODELS, MOLECULAR; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEINS; QUALITY CONTROL; SOFTWARE;

EID: 13444307044     PISSN: 09074449     EISSN: None     Source Type: Journal    
DOI: 10.1107/S0907444904026460     Document Type: Article

References (56)

1. Alexandrov, N. N. (1996). Protein Eng. pp. 727-732.
2. Barakat, D. W. & Dean, P. M. J. (1991). Comput. Aided Mol. Des. 5, 107-117.
3. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G, Bhat, T. N., Weissig, H., Shindyalov, I. N. & Bourne, P. E. (2000). Nucleic Acids Res. pp. 235-242.
4. Bessonov, Y. E. (1985). Vychisl. Sistemy, 112, 3-22.
5. Bron, C. & Kerbosch, J. (1973). Commun. ACM, 16, 575-577.
6. Chotia, C. (1992). Nature (London), 357, 543-544.
7. Chotia, C. & Lesk, A. M. (1986). EMBO J. 5, 823-826.
8. Collaborative Computational Project, Number 4 (1994). Acta Cryst. D50, 760-763.
9. Falicov, A. & Cohen, F. E. (1996). J. Mol. Biol. 258, 871-892.
10. Flores, T. P., Orengo, C. A., Moss, D. C. & Thornton, J. M. (1993). Protein Sci. 2 1811-1826.
11. Gardiner, E. J., Willett, P. & Artymiuk, P. J. (2000). J. Chem. Inf. Comput. Sci. 40, 273-279.
12. Gerstein, M. & Levitt, M. (1996). Proceedings of the Fourth International Conference on Intelligent Systems for Molecular Biology, pp. 59-67. Menlo Park, California: AAAI Press.
13. Gerstein, M. & Levitt, M. (1998). Protein Sci. 7, 445-456.
14. Gibrat, J.-F., Madej, T. & Bryant, S. H. (1996). Curr. Opin. Struct. Biol. 6, 377-385.
15. Godzik, A. & Skolnick, J. (1994). Comput. Appl. Biosci. 10, 587-596.
16. Grindley, H. M., Artymiuk, P. J., Rice, D. W. & Willett, P. J. (1993). Mol. Biol. 229, 707-721.
17. Holm, L. & Sander, C. (1993). J. Mol. Biol. 233, 123-138.
18. Hubbard, T. J. P. & Blundell, T. L. (1987). Protein Eng. 1, 159-171.
19. Hutchinson, E. G. & Thornton, J. M. (1996). Protein Sci. 5, 212-220.
20. Jung, J. & Lee, B. (2000). Protein Eng. 13, 535-543.
21. Kabsch, W. (1976). Acta Cryst. A32, 922-923.
22. Kabsch, W. (1978). Acta Cryst. A34, 827-828.
23. Kagawa, W., Kurumizaka, H., Ishitani, R., Fukai, S., Nureki, O., Shibata, S. & Yokoyama, S. (2002). Mol. Cells, 10, 359.
24. Kato, H. & Takahashi, Y. J. (2001). Chem. Softw. 7, 161-170.
25. Kleywegt, G. J. & Jones, T. A. (1994). CCP4/ESF-EACBM Newsl. Protein Crystallogr. 31, 9-14.
26. Kleywegt, G. J. & Jones, T. A. (1997). Methods Enzymol. 277, 525-545.
27. Kraulis, P. J. (1991). J. Appl. Cryst. 24, 946-950.
28. Krissinel, E. & Henrick, K. (2004). Softw. Pract. Exp. 34. 591-607.
29. Krissinel, E. B., Winn, M. D., Ballard, C. C., Ashton, A. W., Patel, P., Potterton, E. A., McNicholas, S. J., Cowtan, K. D. & Emsley, P. (2004). Acta Cryst. D60, 2250-2255.
30. Leluk, J., Konieczny, L. & Roterman, I. (2003). Bioinformatics, 19, 117-124.
31. Lesk, A. M. (1986). Acta Cryst. A42, 110-113.
32. Levi, G. (1972). Calcolo, 9, 341-354.
33. McLachlan, A. D. (1972). Acta Cryst. A28, 656-657.
34. Merritt, E. A. & Bacon, D. J. (1997). Methods Enzymol. 277, 505-524.
35. Mitchell, E. M., Artymiuk, P. J., Rice, D. W. & Willett, P. J. (1990). Mol. Biol. 212, 151-166.
36. Mizuguchi, K. & Go, N. (1995). Protein Eng. 8, 353-362.
37. Murzin, A. G., Brenner, S. E., Hubbard, T. & Chothia, C. J. (1995). Mol. Biol. 247 536-540.
38. Orengo, C. A. & Taylor, W. R. (1996). Methods Enzymol. 266, 617-635.
39. Raymond, J. & Willett, P. J. (2002). Comput. Aided Mol. Des. 16, 521-533.
40. Raymond, J. W., Gardiner, E. J. & Willett, P. J. (2002). Chem. Inf. Comput. Sci. 42, 305-316.
41. Rouvray, D. H., Balaban, A. T., Wilson, R. J. & Beineke, L. W. (1979). Editors. Applications of Graph Theory, pp. 177-221. NewYork: Academic Press.
42. Russell, R. B. & Barton, G. J. (1992). Proteins, 14, 309-323.
43. Russell, R. B. & Barton, G. J. (1994). J. Mol. Biol. 244, 332-350.
44. Russell, R. B., Saqi, M. A. S., Sayle, R. A., Bates, P. A. & Sternberg, M. J. E. (1997). J. Mol. Biol. 269, 423-439.
45. Ryter, J. M. & Schultz, S. C. (1998). EMBO J. 17, 7505-7513.
46. Sali, A. & Blundell, T. J. (1990). Mol. Biol. 212, 403-428.
47. Sevcik, J., Dodson, E. J. & Dodson, G. G. (1991). Acta Cryst. B47, 240-253.
48. Shearer, K., Bunke, H. & Venkatesh, S. (2001). Pattern Recognit. 34, 1075-1091.
49. Shindyalov, I. N. & Bourne, P. E. (1998). Protein Eng. 11, 739-747.
50. Singh, A. P. & Brutlag, D. L. (1997). Proceedings of the International Conference on Intelligent Systems for Molecular Biology ISMB-97, pp. 284-293. Halkidiki, Greece: AAAI Press.
51. Smith, T. F. & Waterman, M. S. (1981). J. Mol. Biol. 147, 195-197.
52. Subbiah, S., Laurents, D. V. & Levitt, M. (1993). Curr. Biol. 3, 141-148.
53. Taylor, W. & Orengo, C. J. (1989). Mol. Biol. 208, 1-22.
54. Ullman, J. R. (1976). J. Assoc. Comput. Mach. 23, 31-42.
55. Vriend, G. & Sander, C. (1991). Proteins, 11, 52-58.
56. Zuker, M. & Somorjai, R. L. (1989). Bull. Math. Biol. 51, 55-78.