Iterative model building, structure refinement and density modification with the PHENIX AutoBuild wizard

Acta Crystallographica Section D: Biological Crystallography

Volumn 64, Issue 1, 2007, Pages 61-69

  Terwilliger, Thomas C ^a   Grosse Kunstleve, Ralf W ^b   Afonine, Pavel V ^b   Moriarty, Nigel W ^b   Zwart, Peter H ^b   Hung, Li Wei ^a   Read, Randy J ^c   Adams, Paul D ^b  

^a LOS ALAMOS NATIONAL LABORATORY   (United States)

^b LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

^c UNIVERSITY OF CAMBRIDGE   (United Kingdom)

Author keywords

Macromolecular models; Model building; Model completion; PHENIX; Protein Data Bank; Structure refinement

Indexed keywords

PROTEIN;

ALGORITHM; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; CONFERENCE PAPER; MACROMOLECULE; PROTEIN DATABASE; X RAY CRYSTALLOGRAPHY;

ALGORITHMS; CRYSTALLOGRAPHY, X-RAY; DATABASES, PROTEIN; MACROMOLECULAR SUBSTANCES; MODELS, MOLECULAR; PROTEINS; SOFTWARE;

EID: 37349103121     PISSN: 09074449     EISSN: 13990047     Source Type: Journal    
DOI: 10.1107/S090744490705024X     Document Type: Conference Paper

References (31)

1. Adams, P. D., Grosse-Kunstleve, R. W., Hung, L.-W., Ioerger, T. R., McCoy, A. J., Moriarty, N. W., Read, R. J., Sacchettini, J. C., Sauter, N. K. & Terwilliger, T. C. (2002). Acta Cryst. D58, 1948-1954.
2. Afonine, P. V., Grosse-Kunstleve, R. W. & Adams, P. D. (2005a). Acta Cryst. D61, 850-855.
3. Afonine, P. V., Grosse-Kunstleve, R. W. & Adams, P. D. (2005b). CCP4 Newsl. 42, contribution 8.
4. Branden, C. I. & Jones, T. A. (1990). Nature (London), 343, 687-689.
5. Chaudhuri, B. N., Kleywegt, G. J., Björkman, J., Lehman-McKeeman, L. D., Oliver, J. D. & Jones, T. A. (1999). Acta Cryst. D55, 753-762.
6. DePristo, M. A., de Bakker, P. I. W., Johnson, R. J. K. & Blundell, T. L. (2005). Structure, 13, 1311-1319.
7. DiMaio, F., Shavlik, J. & Phillips, G. N. (2006). Bioinformatics, 22, e81-e89.
8. Grosse-Kunstleve, R. W., Sauter, N. K. & Adams, P. D. (2004). IUCr Comput. Commission Newsl. 3, 22-31.
9. Hendrickson, W. A. & Lattman, E. E. (1970). Acta Cryst. B26, 136-143.
10. Hirshfeld, F. L. (1976). Acta Cryst. A32, 239-244.
11. Jensen, L. H. (1997). Methods Enzymol. 277, 353-366.
12. Kearsley, S. K. (1989). Acta Cryst. A45, 208-210.
13. Kuser, P. R., Franzoni, L., Ferrari, E., Spisni, A. & Polikarpov, I. (2001). Acta Cryst. D57, 1863-1869.
14. Liu, D. C. & Nocedal, J. (1989). Math. Program. 45, 503-528.
15. Lovell, S. C., Word, J. M., Richardson, J. S. & Richardson, D. C. (2000). Proteins, 40, 389-408.
16. McCoy, A. J., Grosse-Kunstleve, R. W., Storoni, L. C. & Read, R. J. (2005). Acta Cryst. D61, 458-464.
17. Needleman, S. & Wunsch, C. (1970). J. Mol. Biol. 48, 443-453.
18. Ondráček, J. (2005). Acta Cryst. A61, C163.
19. Pannu, N. S., Murshudov, G. N., Dodson, E. J. & Read, R. J. (1998). Acta Cryst. D54, 1285-1294.
20. Perrakis, A., Morris, R. & Lamzin, V. S. (1999). Nature Struct. Biol. 6, 458-463.
21. Read, R. J. (1986). Acta Cryst. A42, 140-149.
22. Schneider, T. (1996). Proceedings of the CCP4 Study Weekend. Macromolecular Refinement, edited by E. Dodson, M. Moore, A. Ralph & S. Bailey, pp. 133-144.Warrington: Daresbury Laboratory.
23. Smith, T. F. & Waterman, M. S. (1981). J. Mol. Biol. 147, 195-197.
24. Storoni, L. C., McCoy, A. J. & Read, R. J. (2004). Acta Cryst. D60, 432-438.
25. Terwilliger, T. C. (2000). Acta Cryst. D56, 965-972.
26. Terwilliger, T. C. (2001). Acta Cryst. D57, 1755-1762.
27. Terwilliger, T. C. (2002). Acta Cryst. D58, 2082-2086.
28. Terwilliger, T. C. (2003a). Acta Cryst. D59, 38-44.
29. Terwilliger, T. C. (2003b). Acta Cryst. D59, 1174-1182.
30. Terwilliger, T. C. (2003c). Acta Cryst. D59, 1688-1701.
31. Urzhumtsev, A. G., Skovoroda, T. P. & Lunin, V. Y. (1996). J. Appl. Cryst. 29, 741-744.