Databases in protein crystallography

Acta Crystallographica Section D: Biological Crystallography

Volumn 54, Issue 6 I, 1998, Pages 1119-1131

  Kleywegt, Gerard J ^a   Jones, T Alwyn ^a  

^a UPPSALA UNIVERSITY   (Sweden)

Author keywords

[No Author keywords available]

Indexed keywords

CHEMICAL STRUCTURE; CONFERENCE PAPER; CRYSTALLOGRAPHY; DATA BASE; FACTUAL DATABASE; PROTEIN CONFORMATION; REPRODUCIBILITY;

CRYSTALLOGRAPHY; DATABASE MANAGEMENT SYSTEMS; DATABASES, FACTUAL; MODELS, MOLECULAR; PROTEIN CONFORMATION; REPRODUCIBILITY OF RESULTS;

EID: 0032215320     PISSN: 09074449     EISSN: None     Source Type: Journal    
DOI: 10.1107/S0907444998007100     Document Type: Conference Paper

References (79)

1. Aalten, D. M. F. van, Bywater, R., Findlay, J. B. C., Hendlich, M., Hooft, R. W. W. & Vriend, G. (1996). J. Comput. Aided Mol. Design. 10, 255-262.
2. Allen, F. H., Bellard, S., Brice, M. D., Cartwright, B. A., Doubleday, A., Higgs, H., Hummelink, T., Hummelink-Peters, B. G., Kennard, O., Motherwell, W. D. S., Rodgers, J. R. & Watson, D. G. (1979). Acta Cryst. B35, 2331-2339.
3. Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. II, S1-S19.
4. Altschul, S. F., Gish, W., Miller, W., Myers, E. W. & Lipman, D. J. (1990). J. Mol. Biol. 215, 403-410.
5. Artymiuk, P. J., Poirrette, A. R., Grindley, H. M., Rice, D. W. & Willett, P. (1994). J. Mol. Biol. 243, 327-344.
6. Bairoch, A. & Apweiler, R. (1997). Nucleic Acids Res. 25, 31-36.
7. Bairoch, A. & Bucher, P. (1994). Nucleic Acids Res. 22, 3583-3589.
8. Bernstein, F. C., Koetzle, T. F., Williams, G. J. B., Meyer Jr, E. F., Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T. & Tasumi, M. (1977). J. Mol. Biol. 112, 535-542.
9. Brünger, A. T. (1992). Nature (London), 355, 472-475.
10. Brünger, A. T. (1993). Acta Cryst. D49, 24-36.
11. Brünger, A. T., Adams, P. D., Clore, G. M., Gros, P., Grosse-Kunstleve, R. W., Jiang, J.-S., Kuszewski, J., Nilges, M., Pannu, N. S., Read, R. J., Rice, L.M., Simonson, T. & Warren, G. L. (1998). Acta Cryst. D54, 905-921.
12. Denson, D. A., Boguski, M. S., Lipman, D. J. & Ostell, J. (1997). Nucleic Acids Res. 25, 1-6.
13. Divne, C., Ståhlberg, J., Reinikainen, T., Ruohonen, L., Pettersson, G., Knowles, J. K. C., Teeri, T. T. & Jones, T. A. (1994). Science, 265, 524-528.
14. Editorial (1997). Nature Struct. Biol. 4, 961-964.
15. Engh, R. A. & Huber, R. (1991). Acta Cryst. A47, 392-400.
16. Greer, J. (1974). J. Mol. Biol. 82, 279-301.
17. Greer, J. (1981). J. Mol. Biol. 153, 1027-1042.
18. Greer, J. (1985). Methods Enzymol. 115, 206-224.
19. Gribskov, M., Lüthy, R. & Eisenberg, D. (1990). Methods Enzymol. 183, 146-159.
20. Gribskov, M., McLachlan, A. D. & Eisenberg, D. (1987). Proc. Natl Acad. Sci. USA, 84, 4355-4358.
21. Gribskov, M. & Veretnik, S. (1996). Methods Enzymol. 266, 198-212.
22. Harel, M., Kleywegt, G. J., Ravelli, R. B. G., Silman, I. & Sussman, J. L. (1995). Structure, 3, 1355-1366.
23. Heikinheimo, P., Lehtonen, J., Baykov, A., Lahti, R., Cooperman, B. S. & Goldman, A. (1996). Structure, 4, 1491-1508.
24. Hendrickson, W. A. & Konnert, J. H. (1980). In Computing in Crystallography, edited by R. Diamond, S. Ramaseshan & K. Venkatesan, pp. 13.01-13.25. Bangalore: Indian Academy of Science.
25. Henikoff, S. & Henikoff, J. G. (1992). Proc. Nutl Acad. Sci. USA, 89, 10915-10919.
26. Herzberg, O. & Moult, J. (1991). Proteins Struct. Funct. Genet. 11, 223-229.
27. Hobohm, U. & Sander, C. (1994). Protein Sci. 3, 522-524.
28. Holm, L. & Sander, C. (1994). Proteins Struct. Funct. Genet. 19, 165-173.
29. Holm, L. & Sander, C. (1996). Methods Enzymol. 266, 653-662.
30. Hooft, R. W., Sander, C. & Vriend, G. (1997). Comput. Appl. Biosci. 13, 425-430.
31. James, M. N. G. & Sielecki, A. R. (1983). J. Mol. Biol. 163, 299-361.
32. Janin, J., Wodak, S., Levitt, M. & Maigret, B. (1978). J. Mol. Biol. 125, 357-386.
33. Jones, T. A. (1978). J. Appl. Cryst. 11, 268-272.
34. Jones, T. A. (1985). Methods Enzymol. 115, 157-171.
35. Jones, T. A. & Kjeldgaard, M. (1994). In From First Map to Final Model, edited by S. Bailey, R. Hubbard & D. A. Waller, pp. 1-13. Warrington: Daresbury Laboratory.
36. Jones, T. A. & Kjeldgaard, M. (1997). Methods Enzymol. 277, 173-198.
37. Jones, T. A., Kleywegt, G. J. & Brünger, A. T. (1996). Nature (London), 383, 18-19.
38. Jones, T. A. & Thirup, S. (1986). EMBO J. 5, 819-822.
39. Jones, T. A., Zou, J. Y., Cowan, S. W. & Kjeldgaard, M. (1991). Acta Cryst. A47, 110-119.
40. Kendrew, J. C., Dickerson, R. E., Strandberg, B. E., Hart, R. G., Davies, D. R., Phillips, D. C. & Shore, V. C. (1960). Nature (London), 185, 422-427.
41. Kleywegt, G. J. (1996). Acta Cryst. D52, 842-857.
42. Kleywegt, G. J. (1997). J. Mol. Biol. 273, 371-376.
43. Kleywegt, G. J. (1998). Submitted.
44. Kleywegt, G. J. & Brünger, A. T. (1996). Structure, 4, 897-904.
45. Kleywegt, G. J., Hoier, H. & Jones, T. A. (1996). Acta Cryst. D52, 858-863.
46. Kleywegt, G. J. & Jones, T. A. (1994). In From First Map to Final Model, edited by S. Bailey, R. Hubbard & D. A. Waller, pp. 59-66. Warrington: Daresbury Laboratory.
47. Kleywegt, G. J. & Jones, T. A. (1995a). Structure. 3, 535-540.
48. Kleywegt, G. J. & Jones, T. A. (1995b). In Making the Most of your Model, edited by W. N. Hunter, J. M. Thornton & S. Bailey, pp. 11-24. Warrington: Daresbury Laboratory.
49. Kleywegt, G. J. & Jones, T. A. (1996a). Acta Cryst. D52, 829-832.
50. Kleywegt, G. J. & Jones, T. A. (1996b). Structure, 4, 1395-1400.
51. Kleywegt, G. J. & Jones, T. A. (1997a). Acta Cryst. D53. 179-185.
52. Kleywegt, G. J. & Jones, T. A. (1997b). Methods Enzymol. 277, 208-230.
53. Kleywegt, G. J. & Jones, T. A. (1997c). Methods Enzymol. 277, 525-545.
54. Kleywegt, G. J., Zou, J.Y., Divne, C., Davies, G. J., Sinning, I., Ståhlberg, J., Reinikainen, T., Srisodsuk, M., Teeri, T. T. & Jones, T. A. (1997). J. Mol. Biol. 272, 383-397.
55. Kraulis, P. J. & Jones, T. A. (1987). Proteins Struct. Funct. Genet. 2, 188-201.
56. Kuszewski, J., Gronenborn, A. M. & Clore, G. M. (1996). Protein Sci. 5, 1067-1080.
57. Kuszewski, J., Gronenborn, A. M. & Clore, G. M. (1997). J. Magn. Reson. 125, 171-177.
58. Laskowski, R. A., MacArthur, M. W., Moss, D. S. & Thornton, J. M. (1993). J. Appl. Cryst. 26, 283-291.
59. Laskowski, R. A., Moss, D. S. & Thornton, J. M. (1993). J. Mol. Biol. 231, 1049-1067.
60. Lesk, A. M. (1979). Commun. ACM, 22, 219-224.
61. MacArthur, M. W., Laskowski, R. A. & Thornton, J. M. (1994). Curr. Opin. Struct. Biol. 4, 731-737.
62. Matte, A., Goldie, H., Sweet, R. M., & Delbaere, L. T. J. (1996). J. Mol. Biol. 256, 126-143.
63. Morris, A. L., MacArthur, M. W., Hutchinson, E. G. & Thornton, J. M. (1992). Proteins Struct. Funct. Genet. 12, 345-364.
64. Noble, M. E. M., Zeelen, J. P., Wieringa, R. K., Mainfroid, V., Goraj, K., Gohimont, A. C. & Martial, J. A. (1993). Acta Cryst. D49, 403-417.
65. Oldfield, T. J. & Hubbard, R. E. (1994). Proteins Struct. Funct. Genet. 18, 324-337.
66. Oilis, D. L., Cheah, E., Cygler, M., Dijkstra, B. W., Frolow, E., Franken, S. M., Harel, M., Remington, S. J., Silman, I., Schrag, J., Sussman, J. S., Verschueren, K. H. G. & Goldman, A. (1992). Protein Eng. 5, 197-211.
67. Parkinson, G., Vojtechovsky, J., Clowney, L., Brünger, A. T. & Berman, H. M. (1996). Acta Cryst. D52, 57-64.
68. Pearson, W. R. & Lipman, D. J. (1988). Proc. Natl Acad. Sci. USA, 85. 2444-2448.
69. Phillips, D. C. (1970). British Biochemistry, Past and Present, edited by T. W. Goodwin, pp. 11-28. London: Academic Press.
70. Ponder, J. W. & Richards, F. M. (1987). J. Mol. Biol. 193, 775-791.
71. Priestle, J. P. (1994). Structure, 2, 911-913.
72. Ramachandran, G. N., Ramakrishnan, C. & Sasisekharan, V. (1963). J. Mol. Biol. 7, 95-99.
73. Ramakrishnan, C. & Ramachandran, G. N. (1965). Biophys. J. 5, 909-933.
74. Sevcik, J., Dauter, Z., Lamzin, V. S. & Wilson, K. S. (1996). Acta Cryst. D52, 327-344.
75. Sonnhammer, E. L. L. & Kahn, D. (1994). Protein Sci. 3, 482-492.
76. Vriend, G. & Sander, C. (1993). J. Appl. Cryst. 26, 47-60.
77. Watenpaugh, K. D., Sicker, L. C., Herriott, J. R. & Jensen, L. H. (1973). Acta Cryst. B29, 943-956.
78. Willett, P. (1987). J. Chemometrics. 1, 139-155.
79. Zou, J. Y. & Mowbray, S. L. (1994). Acta Cryst. D50, 237-249.