Performance of phased rotation, conformation and translation function: Accurate protein model building with tripeptidic and tetrapeptidic fragments

Acta Crystallographica Section D: Biological Crystallography

Volumn 66, Issue 9, 2010, Pages 1012-1023

  Pavelčík, František ^a   Václavík, Jií ^a  

^a UNIVERSITY OF VETERINARY AND PHARMACEUTICAL SCIENCES   (Czech Republic)

Author keywords

automatic model building; conformation function; flexible group model; generalized atoms; real space refinement; rotation function; tetrapeptides; translation function; tripeptides

Indexed keywords

OLIGOPEPTIDE; PROTEIN;

ARTICLE; BIOLOGICAL MODEL; CHEMISTRY; METHODOLOGY; PROTEIN CONFORMATION; X RAY CRYSTALLOGRAPHY; PROCEDURES;

CRYSTALLOGRAPHY, X-RAY; MODELS, BIOLOGICAL; OLIGOPEPTIDES; PROTEIN CONFORMATION; PROTEINS;

EID: 77956553636     PISSN: 09074449     EISSN: 13990047     Source Type: Journal    
DOI: 10.1107/S0907444910030234     Document Type: Article

References (43)

1. Binda, C., Coda, A., Aliverti, A., Zanetti, G. & Mattevi, A. (1998). Acta Cryst. D54, 1353-1358.
2. Brunger, A. T., DeLaBarre, B., Davies, J. M. & Weis, W. I. (2009). Acta Cryst. D65, 128-133.
3. Chapman, M. S. (1995). Acta Cryst. A51, 69-80.
4. Clemons, W. M. Jr, Davies, C., White, S. W. & Ramakrishnan, V. (1998). Structure, 6, 429-438.
5. Cowtan, K. (2006). Acta Cryst. D62, 1002-1011.
6. Cowtan, K. (2008). Acta Cryst. D64, 83-89.
7. Deka, R. K., Machius, M., Norgard, M. V. & Tomchick, D. R. (2002). J. Biol. Chem. 277, 41857-41864.
8. Diamond, R. (1971). Acta Cryst. A27, 436-452.
9. DiMaio, F., Kondrashov, D. A., Bitto, E., Soni, A., Bingman, C. A., Phillips, G. N. & Shavlik, J. W. (2007). Bioinformatics, 23, 2851-2858.
10. DiMaio, F., Shavlik, J. W. & Phillips, G. N. (2006). Bioinformatics, 22, e81-e89.
11. Dodson, E. J. (2004). Personal communication.
12. Doyle, D. A., Lee, A., Lewis, J., Kim, E., Sheng, M. & MacKinnon, R. (1996). Cell, 85, 1067-1076.
13. Friedman, J. M. (1999). Comput. Chem. 23, 9-23.
14. Hattne, J. & Lamzin, V. S. (2008). Acta Cryst. D64, 834-842.
15. Hovmöller, S., Zhou, T. & Ohlson, T. (2002). Acta Cryst. D58, 768-776.
16. Jones, T. A. & Kjeldgaard, M. (1997). Methods Enzymol. 277, 173-208.
17. Joosten, K., Cohen, S. X., Emsley, P., Mooij, W., Lamzin, V. S. & Perrakis, A. (2008). Acta Cryst. D64, 416-424.
18. Kleywegt, G. J. & Jones, T. A. (1997). Acta Cryst. D53, 179-185.
19. Korostelev, A., Bertram, R. & Chapman, M. S. (2002). Acta Cryst. D58, 761-767.
20. Levinthal, C. (1968). J. Chim. Phys. Phys. Chim. Biol. 65, 44-45.
21. Lovell, S. C., Word, J. M., Richardson, J. S. & Richardson, D. C. (2000). Proteins, 40, 389-408.
22. Martinez-Oyanedel, J., Choe, H. W., Heinemann, U. & Saenger, W. (1991). J. Mol. Biol. 222, 335-352.
23. Morgan, H. L. (1965). J. Chem. Doc. 5, 107-113.
24. Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255.
25. Oakley, A. J., Lo Bello, M., Nuccetelli, M., Mazzetti, A. P. & Parker, M. W. (1999). J. Mol. Biol. 291, 913-926.
26. Pavelcik, F. (2003). Acta Cryst. A59, 487-494.
27. Pavelcik, F. (2004). Acta Cryst. D60, 1535-1544.
28. Pavelcik, F. (2006a). J. Appl. Cryst. 39, 483-486.
29. Pavelcik, F. (2006b). J. Appl. Cryst. 39, 287.
30. Pavelcik, F. (2008). J. Appl. Cryst. 41, 62-67.
31. Pavelcik, F. & Pavelcikova, P. (2007). Acta Cryst. D63, 1162-1168.
32. Pavelcik, F. & Schneider, B. (2008). Acta Cryst. D64, 620-626.
33. Pavelcik, F. & Vanco, J. (2006). J. Appl. Cryst. 39, 315-319.
34. Pavelcik, F., Zelinka, J. & Otwinowski, Z. (2002). Acta Cryst. D58, 275-283.
35. Perrakis, A., Morris, R. & Lamzin, V. S. (1999). Nature Struct. Biol. 6, 458-463.
36. Sevcik, J., Dodson, E. J. & Dodson, G. G. (1991). Acta Cryst. B47, 240-253.
37. Singh, N., Jabeen, T., Sharma, S., Somvanshi, R. K., Dey, S., Srinivasan, A. & Singh, T. P. (2006). Acta Cryst. D62, 410-416.
38. Smith, G. D., Pangborn, W. & Blessing, R. H. (2001). Acta Cryst. D57, 1091-1100.
39. Terwilliger, T. C. (2003a). Acta Cryst. D59, 38-44.
40. Terwilliger, T. C. (2003b). Acta Cryst. D59, 45-49.
41. Tomchick, D. R. (2001). Personal communication.
42. Yamano, A., Heo, N. H. & Teeter, M. M. (1997). J. Biol. Chem. 272, 9597-9600.
43. Zou, J.-Y. & Jones, T. A. (1996). Acta Cryst. D52, 833-841.