Identifying non-crystallographic symmetry in protein electron-density maps: A feature-based approach

Acta Crystallographica Section D: Biological Crystallography

Volumn 62, Issue 9, 2006, Pages 1012-1021

  Pai, Reetal ^a   Sacchettini, James ^a   Ioerger, Thomas ^a  

^a TEXAS A AND M UNIVERSITY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

PHOSPHOGLYCERATE DEHYDROGENASE; PROTEIN;

ALGORITHM; ARTICLE; AUTOMATED PATTERN RECOGNITION; BIOLOGY; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; ELECTRON; ENZYMOLOGY; METHODOLOGY; MYCOBACTERIUM TUBERCULOSIS; PROTEIN CONFORMATION; PROTEIN SECONDARY STRUCTURE; REPRODUCIBILITY; STATISTICAL MODEL; X RAY CRYSTALLOGRAPHY;

ALGORITHMS; COMPUTATIONAL BIOLOGY; CRYSTALLOGRAPHY, X-RAY; ELECTRONS; MODELS, MOLECULAR; MODELS, STATISTICAL; MOLECULAR CONFORMATION; MYCOBACTERIUM TUBERCULOSIS; PATTERN RECOGNITION, AUTOMATED; PHOSPHOGLYCERATE DEHYDROGENASE; PROTEIN CONFORMATION; PROTEIN STRUCTURE, SECONDARY; PROTEINS; REPRODUCIBILITY OF RESULTS;

EID: 33748364126     PISSN: 09074449     EISSN: 13990047     Source Type: Journal    
DOI: 10.1107/S0907444906023158     Document Type: Article

References (40)

1. Bailey, S., Dodson, E. & Phillips, S. (1988). Editors. Proceedings of the CCP4 Study Weekend. Improving Protein Phases. Warrington: Daresbury Laboratory.
2. Bricogne, G. (1974). Acta Cryst. A30, 395-405.
3. Brünger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., Gros, P., Grosse-Kunstleve, R. W., Jiang, J.-S., Kuszewski, J., Nilges, N., Pannu, N. S., Read, R. J., Rice, L. M., Simonson, T. & Warren, G. L. (1998). Acta Cryst. D54, 905-921.
4. Burling, F. T., Weis, W. I., Flaherty, K. M. & Brünger, A. T. (1996). Science, 271, 72-77.
5. Coutsias, E. A., Seok, C. & Dill, K. A. (2004). J. Comput. Chem. 25, 1849-1857.
6. Cowan, S. W., Newcomer, M. E. & Jones, T. A. (1993). J. Mol. Biol. 230, 1225-1246.
7. Cowtan, K. D. & Main, P. (1993). Acta Cryst. D49, 148-157.
8. Crowther, R. A. (1967). Acta Cryst. A22, 758-764.
9. Dey, S., Grant, G. A. & Sacchettini, J. C. (2005). J. Biol. Chem. 280, 14892-14899.
10. Doyle, D. A., Lee, A., Lewis, J., Kim, E., Sheng, M. & MacKinnon, R. (1996). Cell, 85, 1067-1076.
11. Duda, R. O. & Hart, P. E. (1973). Pattern Classification and Scene Analysis. New York: Wiley.
12. Eicken, C., Sharma, V., Klabunde, T., Lawrenz, M. B., Hardham, J.M., Norris, S. J. & Sacchettini, J. C. (2002). J. Biol. Chem. 277, 21691-21696.
13. Gopal, K., Pai, R, Ioerger, T. R., Romo, T. & Sacchettini, J. C. (2003). Proceedings of the Fifteenth Conference on Innovative Applications of Artificial Intelligence, pp. 93-100. Menlo Park, CA, USA: AAAI.
14. Gopal, K., Romo, T. D., Sacchettini, J. C. & Ioerger, T. R. (2004). Computational Systems Bioinformatics Conference, pp. 255-265. Los Alamitos, CA, USA: IEEE.
15. Huang, C., Smith, C. V., Glickman, M. S., Jacobs, W. R. & Sacchettini, J. C. (2002). J. Biol. Chem. 277, 11559-11569.
16. Ioerger, T. R. & Sacchettini, J. C. (2002). Acta Cryst. D58, 2043-2054.
17. Ioerger, T. R. & Sacchettini, J. C. (2003). Methods Enzymol. 374, 244-270.
18. Jiang, J., Zhang, Y., Kranier, A. R. & Xu, R. M. (1999). Proc. Natl Acad. Sci. USA, 96, 3572-3577.
19. Kabsch, W. (1978). Acta Cryst. A34, 827-828.
20. Kleywegt, G. J. & Jones, T. A. (1994). Proceedings of the CCP4 Study Weekend. From First Map to Final Model, edited by S. Bailey, R. Hubbard & D. Waller, pp. 59-66. Warrington: Daresbury Laboratory.
21. Lu, G. (1999). J. Appl. Cryst. 32, 365-368.
22. Lunin, V. Yu. & Woolfson, M. M. (1993). Acta Cryst. D49, 530-533.
23. McCoy, A. J., Grosse-Kunstleve, R. W., Storoni, L. C. & Read, R. J. (2005). Acta Cryst. D61, 458-464.
24. Mackay, A. L. (1984). Acta Cryst. A40, 165-166.
25. McKee, E., Kanbi, L. D., Childs, K. C., Grosse-Kunstleve, R. W., Adams, P. A., Sacchettini, J. C. & Ioerger, T. R. (2005). Acta Cryst. D61, 1514-1520.
26. Main, P. & Rossmann, M. G. (1966). Acta Cryst. 21, 67-72.
27. Muirhead, H., Cox, J. M., Mazzarella, L. & Perutz, M. F. (1967). J. Mol. Biol. 28, 117-156.
28. Navaza, J. (1994). Acta Cryst. A50, 157-163.
29. Rossmann, M. G. (1972). The Molecular Replacement Method. New York: Gordon & Breach.
30. Rossmann, M. G. & Blow, D. M. (1962). Acta Cryst. 15, 24-31.
31. Rozwarski, D., Diederichs, K., Hecht, R., Boone, T. & Karplus, P. (1996). Proteins, 26, 304-313.
32. Sharma, V., Sharma, S., Bentrup, K. H., McKinney, J. D., Russell, D. G., Jacobs, W. J. & Sacchettini, J. C. (2000). Nature Struct. Biol. 7, 663-668.
33. Shin, D. H., Choi, I.-G., Busso, D., Jancarik, J., Yokota, H., Kim, R. & Kim, S.-H. (2004). Acta Cryst. D60, 903-911.
34. Shin, D. H., Roberts, A., Jancarik, J., Yokota, H., Kim, R., Wemmer, D. E. & Kim, S.-H. (2003). Protein Sci. 12, 1464-1472.
35. Tanner, J. J., Lei, B., Tu, S. C. & Krause, K. L. (1996). Biochemistry, 35, 13531.
36. Terwilliger, T. C. (2000). Acta Cryst. D56, 965-972.
37. Terwilliger, T. C. (2002a). Acta Cryst. D58, 2213-2215.
38. Terwilliger, T. C. (2002b). Acta Cryst. D58, 2082-2086.
39. Turner, M. A., Yuan, C. S., Borchardt, R. T., Hershfield, M. S., Smith, G. D. & Howell, P. L. (1998). Nature Struct. Biol. 5, 369.
40. Vellieux, F. M. D. & Read, R. J. (1997). Methods Enzymol. 277, 18-53.