Model preparation in MOLREP and examples of model improvement using X-ray data

Acta Crystallographica Section D: Biological Crystallography

Volumn 64, Issue 1, 2007, Pages 33-39

  Lebedev, Andrey A ^a   Vagin, Alexei A ^a   Murshudov, Garib N ^a  

^a UNIVERSITY OF YORK   (United Kingdom)

Author keywords

Model preparation; Molecular replacement; MOLREP

Indexed keywords

PROTEIN;

ALGORITHM; AMINO ACID SEQUENCE; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER PROGRAM; COMPUTER SIMULATION; CONFERENCE PAPER; CRYSTALLIZATION; GENETICS; METHODOLOGY; SEQUENCE ALIGNMENT; STRUCTURAL HOMOLOGY; X RAY CRYSTALLOGRAPHY;

ALGORITHMS; AMINO ACID SEQUENCE; COMPUTER SIMULATION; CRYSTALLIZATION; CRYSTALLOGRAPHY, X-RAY; MODELS, MOLECULAR; PROTEINS; SEQUENCE ALIGNMENT; SOFTWARE; STRUCTURAL HOMOLOGY, PROTEIN;

EID: 37349121133     PISSN: 09074449     EISSN: 13990047     Source Type: Journal    
DOI: 10.1107/S0907444907049839     Document Type: Conference Paper

References (29)

1. Berman, H. M. et al. (2002). Acta Cryst. D58, 899-907.
2. Brünger, A. T., Adams, P. D., Clore, G. M., DeLano, W. L., 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.
3. Chothia, C. (1992). Nature (London), 357, 543-544.
4. Collaborative Computational Project, Number 4 (1994). Acta Cryst. D50, 760-763.
5. Emsley, P. & Cowtan, K. (2004). Acta Cryst. D60, 2126-2132.
6. Fiser, A. & Sali, A. (2003). Methods Enzymol. 374, 461-491.
7. Gonzales, R. C. & Woods, R. E. (2002). Digital Image Processing. Upper Saddle River, New Jersey: Prentice Hall.
8. Isupov, M. N., Brindley, A. A., Hollingsworth, E. J., Murshudov, G. N., Vagin, A. A. & Littlechild, J. A. (2004). Acta Cryst. D60, 1879-1882.
9. Keegan, R. M. & Winn, M. D. (2008). Acta Cryst. D64, 119-124.
10. Krissinel, E. & Henrick, K. (2004). Acta Cryst. D60, 2256-2268.
11. Krissinel, E. & Henrick, K. (2005). CompLife 2005, edited by M. R. Berthold, R. Glen, K. Diederichs, O. Kohlbacher & I. Fischer, pp. 163-174. Berlin, Heidelberg: Springer-Verlag.
12. Lee, B. & Richards, F. M. (1971). J. Mol. Biol. 55, 379-400.
13. Long, F., Vagin, A. A., Young, P. & Murshudov, G. N. (2008). Acta Cryst. D64, 125-132.
14. Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255.
15. Murzin, A. G., Brenner, S. E., Hubbard, T. & Chothia, C. (1995). J. Mol. Biol. 247, 536-540.
16. Navaza, J. (1994). Acta Cryst. A50, 157-163.
17. Needleman, S. B. & Wunsch, C. D. (1970). J. Mol. Biol. 48, 443-453.
18. Read, R. J. (2001). Acta Cryst. D57, 1373-1382.
19. Rye, C. A., Isupov, M. N., Lebedev, A. A. & Littlechild, J. A. (2007). Acta Cryst. D63, 926-930.
20. Sanders, C., Kovalevskiy, O., Sizov, D., Lebedev, A., Isupov, M. N. & Antson, A. A. (2007). Nucleic Acids Res. 35, 6451-6457.
21. Schwarzenbacher, R., Godzik, A., Grzechnik, S. K. & Jaroszewski, L. (2004). Acta Cryst. D60, 1229-1236.
22. Schwarzenbacher, R., Godzik, A. & Jaroszewski, L. (2008). Acta Cryst. D64, 133-140.
23. Schwede, T., Kopp, J., Guex, N. & Peitsch, M. C. (2003). Nucleic Acids Res. 31, 3381-3385.
24. Stubbs, M. T. & Huber, R. (1991). Acta Cryst. A47, 521-526.
25. Suhre, K. & Sanejouand, Y. H. (2004). Nucleic Acids Res. 32, W610-W614.
26. Tong, L. (2001). Acta Cryst. D57, 1383-1389.
27. Vagin, A. A. (1983). PhD thesis. Institute of Crystallography, Moscow, USSR.
28. Vagin, A. A. & Isupov, M. N. (2001). Acta Cryst. D57, 1451-1456.
29. Vagin, A. & Teplyakov, A. (1997). J. Appl. Cryst. 30, 1022-1025.