Re-refinement from deposited X-ray data can deliver improved models for most PDB entries

Acta Crystallographica Section D: Biological Crystallography

Volumn 65, Issue 2, 2009, Pages 176-185

  Joosten, Robbie P ^a   Womack, Thomas ^b   Vriend, Gert ^a   Bricogne, Gérard ^b  

^a RADBOUD UNIVERSITY MEDICAL CENTER   (Netherlands)

^b GLOBAL PHASING LTD   (United Kingdom)

Author keywords

Re refinement

Indexed keywords

ARTICLE; BIOLOGY; COMPUTER PROGRAM; INFORMATION RETRIEVAL; METHODOLOGY; PROTEIN DATABASE; X RAY CRYSTALLOGRAPHY;

COMPUTATIONAL BIOLOGY; CRYSTALLOGRAPHY, X-RAY; DATABASES, PROTEIN; INFORMATION STORAGE AND RETRIEVAL; SOFTWARE;

EID: 58849160465     PISSN: 09074449     EISSN: 13990047     Source Type: Journal    
DOI: 10.1107/S0907444908037591     Document Type: Article

References (34)

1. Asojo, O. A., Afonina, E., Gulnik, S. V., Yu, B., Erickson, J. W., Randad, R., Medjahed, D. & Silva, A. M. (2002). Acta Cryst. D58, 2001-2008.
2. Barta, T. E., Veal, J. M., Rice, J. W., Partridge, J. M., Fadden, R. P., Ma, W., Jenks, M., Geng, L., Hanson, G. J., Huang, K. H., Barabasz, A. F., Foley, B. E., Otto, J. & Hall, S. E. (2008). Bioorg. Med. Chem. Lett. 18, 3517-3521.
3. Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N. & Bourne, P. E. (2000). Nucleic Acids Res. 28, 235-242.
4. Bricogne, G., Blanc, E., Brandl, M., Flensburg, C., Keller, P., Paciorek, W., Roversi, P., Smart, O. S., Vonrhein, C. & Womack, T. (2008). BUSTER-TNT 2.5.1 and autoBUSTER 1.3.1. Global Phasing Ltd, Cambridge.
5. Collaborative Computational Project, Number 4 (1994). Acta Cryst. D50, 760-763.
6. Davis, A. M., At-Gallay, S. A. & Kleywegt, G. J. (2008). Drug Discov. Today, 13, 831-841.
7. Dellisanti, C. D., Yao, Y., Stroud, J. C., Wang, Z. Z. & Chen, L. (2007). Nature Neurosci. 10, 953-962.
8. DePristo, M. A., de Bakker, P. I. W., Johnson, R. J. & Blundell, T. L. (2005). Structure, 13, 1311-1319.
9. Emsley, P. & Cowtan, K. (2004). Acta Cryst. D60, 2126-2132.
10. Engh, R. A. & Huber, R. (1991). Acta Cryst. A47, 392-400.
11. Gregg, K. J., Finn, R., Abbott, D. W. & Boraston, A. B. (2008). J. Biol. Chem. 283, 12604-12613.
12. Henrick, K. et al. (2008). Nucleic Acids Res. 36, D426-D433.
13. Hooft, R. W. W., Vriend, G., Sander, C. & Abola, E. E. (1996). Nature (London), 381, 272.
14. Hoier, H., Schlömann, M., Hammer, A., Glusker, J. P., Carrell, H. L., Goldman, A., Stezowski, J. J. & Heinemann, U. (1994). Acta Cryst. D50, 75-84.
15. Hub, J. S., Salditt, T., Rheinstädter, M. C. & de Groot, B. L. (2007). Biophys. J. 93, 3156-3168.
16. Joosten, R. P. & Vriend, G. (2007). Science, 317, 195-196.
17. Kim, M. I., Kim, H. S., Jung, J. & Rhee, S. (2008). J. Mol. Biol. 380, 636-647.
18. Kleywegt, G. J., Harris, M. R., Zou, J., Taylor, T. C., Wählby, A. & Jones, T. A. (2004). Acta Cryst. D60, 2240-2249.
19. Kleywegt, G. J., Hoier, H. & Jones, T. A. (1996). Acta Cryst. D52, 858-863.
20. Kleywegt, G. J. & Jones, T. A. (2002). Structure, 10, 465-472.
21. Krieger, E., Darden, T., Nabuurs, S. B., Finkelstein, A. & Vriend, G. (2004). Proteins, 57, 678-683.
22. Leinonen, R., Diez, F. G., Binns, D., Fleischmann, W., Lopez, R. & Apweiler, R. (2004). Bioinformatics, 20, 3236-3237.
23. Lütteke, T. & von der Lieth, C. W. (2004). BMC Bioinformatics, 5, 69.
24. Merritt, E. A. & Bacon, D. J. (2007). Methods Enzymol. 277, 505-524.
25. Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255.
26. Nabuurs, S. B., Nederveen, A. J., Vranken, W., Doreleijers, J. F., Bonvin, A. M., Vuister, G. W., Vriend, G. & Spronk, C. A. (2004). Proteins, 55, 483-486.
27. Nabuurs, S. B., Wagener, M. & de Vlieg, J. (2007). J. Med. Chem. 50, 6507-6518.
28. Opaleye, O., Rose, R.-S., Whittaker, M. M., Woo, E.-J., Whittaker, J. W. & Pickersgill, R. W. (2006). J. Biol. Chem. 281, 6428-6433.
29. Parkinson, G., Vojtechovsky, J., Clowney, L., Brünger, A. T. & Berman, H. M. (1996). Acta Cryst. D52, 57-64.
30. Perrakis, A., Morris, R. & Lamzin, V. S. (1999). Nature Struct. Biol. 6, 458-463.
31. Perrakis, A., Sixma, T. K., Wilson, K. S. & Lamzin, V. S. (1997). Acta Cryst. D53, 448-455.
32. Schomaker, V. & Trueblood, K. N. (1968). Acta Cryst. B24, 63-76.
33. Smart, O. S., Brandl, M., Flensburg, C., Keller, P., Paciorek, W., Vonrhein, C., Womack, T. O. & Bricogne, G. (2008). Abstr. Annu. Meet. Am. Crystallogr. Assoc., Abstract TP139, p. 117.
34. Thapper, A., Boer, D. R., Brondino, C. D., Moura, J. J. & Romão, M. J. (2007). J. Biol. Inorg. Chem. 12, 353-366.