Automatic α-helix identification in Patterson maps

Acta Crystallographica Section D: Biological Crystallography

Volumn 68, Issue 1, 2012, Pages 1-12

  Caliandro, Rocco ^a   Dibenedetto, Domenica ^b   Cascarano, Giovanni Luca ^a   Mazzone, Annamaria ^a   Nico, Giovanni ^a  

^a CNR   (Italy)

^b RWTH AACHEN UNIVERSITY   (Germany)

Author keywords

helices; Fourier filtering; Patterson maps

Indexed keywords

PROTEIN;

ALGORITHM; ARTICLE; CHEMICAL STRUCTURE; CHEMISTRY; GENETICS; LABORATORY AUTOMATION; METHODOLOGY; MUTATION; PROTEIN SECONDARY STRUCTURE; PROTEIN TERTIARY STRUCTURE; X RAY CRYSTALLOGRAPHY;

ALGORITHMS; AUTOMATION, LABORATORY; CRYSTALLOGRAPHY, X-RAY; MODELS, MOLECULAR; MUTATION; PROTEIN STRUCTURE, SECONDARY; PROTEIN STRUCTURE, TERTIARY; PROTEINS;

EID: 84857881700     PISSN: 09074449     EISSN: 13990047     Source Type: Journal    
DOI: 10.1107/S0907444911046282     Document Type: Article

References (37)

1. Arnold, K., Bordoli, L., Kopp, J. & Schwede, T. (2006). Bioinformatics, 22, 195-201.
2. Bernstein, F. C., Koetzle, T. F.,Williams, G. J. B., Meyer, E. F. Jr, Brice, M. D., Rodgers, J. R., Kennard, O., Shimanouchi, T. & Tasumi, M. (1977). J. Mol. Biol. 112, 535-542.
3. Blundell, T. L., Jhoti, H. & Abell, C. (2002). Nature Rev. Drug Discov. 1, 45-54.
4. Burla, M. C., Caliandro, R., Camalli, M., Carrozzini, B., Cascarano, G. L., De Caro, L., Giacovazzo, C., Polidori, G., Siliqi, D. & Spagna, R. (2007). J. Appl. Cryst. 40, 609-613.
5. Caliandro, R., Carrozzini, B., Cascarano, G. L., De Caro, L., Giacovazzo, C., Mazzone, A. M. & Siliqi, D. (2006). J. Appl. Cryst. 39, 185-193.
6. Caliandro, R., Carrozzini, B., Cascarano, G. L., Giacovazzo, C., Mazzone, A. M. & Siliqi, D. (2009). Acta Cryst. D65, 477-484.
7. Chang, G. & Lewis, M. (1997). Acta Cryst. D53, 279-289.
8. Cochran, W., Crick, F. H. & Vand, V. (1952). Acta Cryst. 5, 581-586.
9. DeLano, W. L. & Brü nger, A. T. (1995). Acta Cryst. D51, 740-748.
10. Dodson, E. J. & Woolfson, M. M. (2009). Acta Cryst. D65, 881-891.
11. Enkhbayar, P., Damdinsuren, S., Osaki, M. & Matsushima, N. (2008). Comput. Biol. Chem, 32, 307-310.
12. Esposito, L., Vitagliano, L., Sica, F., Sorrentino, G., Zagari, A. & Mazzarella, L. (2000). J. Mol. Biol. 297, 713-732.
13. Franklin, R. E. & Gosling, R. G. (1953). Acta Cryst. 6, 678-685.
14. Franklin, R. E. & Gosling, R. G. (1955). Acta Cryst. 8, 151-156.
15. Frigo, M. & Johnson, S. G. (2005). Proc. IEEE, 93, 216-231.
16. Glykos, N. M. & Kokkinidis, M. (2000). Acta Cryst. D56, 169-174.Glykos, N. M. & Kokkinidis, M. (2003). Acta Cryst. D59, 709-718.
17. Hahn, Th. & Looijenga-Vos, A. (2006). International Tables for Crystallography, Vol. A, 1st online ed., edited by Th. Hahn, pp. 22- 23. Chester: International Union of Crystallography.
18. Harata, K., Abe, Y. & Muraki, M. (1999). J. Mol. Biol. 287, 347-358.
19. Jamrog, D. C., Zhang, Y. & Phillips, G. N. (2003). Acta Cryst. D59, 304-314.
20. Keegan, R. M. & Winn, M. D. (2007). Acta Cryst. D63, 447-457.
21. Kim, S.-H. & Rich, A. (1969). Science, 166, 1621-1624.
22. Kissinger, C. R., Gehlhaar, D. K. & Fogel, D. B. (1999). Acta Cryst. D55, 484-491.
23. Kondo, J., Urzhumtseva, L. & Urzhumtsev, A. (2008). Acta Cryst. D64, 1078-1091.
24. Long, F., Vagin, A. A., Young, P. & Murshudov, G. N. (2008). Acta Cryst. D64, 125-132.
25. Magdoff, B. S., Crick, F. H. C. & Luzzati, V. (1956). Acta Cryst. 9, 156-162.
26. McCoy, A. J., Grosse-Kunstleve, R. W., Adams, P. D., Winn, M. D., Storoni, L. C. & Read, R. J. (2007). J. Appl. Cryst. 40, 658-674.
27. Orengo, C. A., Michie, A. D., Jones, S., Jones, D. T., Swindells,M. B. & Thornton, J. M. (1997). Structure, 5, 1093-1108.
28. Panjikar, S., Parthasarathy, V., Lamzin, V. S.,Weiss, M. S. & Tucker, P. A. (2005). Acta Cryst. D61, 449-457.
29. Potashman, M. H. et al. (2007). J. Med. Chem. 50, 4351-4373.
30. Rigden, D. J., Keegan, R. M. & Winn, M. D. (2008). Acta Cryst. D64, 1288-1291.
31. Rodríguez, D. D., Grosse, C., Himmel, S., Gonzá lez, C., de Ilarduya, I. M., Becker, S., Sheldrick, G. M. & Usó n, I. (2009). Nature Methods, 6, 651-653.
32. Sakurai, T., Rao, S. T., Rubin, J. & Sundaralingam, M. (1971). Science, 172, 1234-1237.
33. Sali, A. & Blundell, T. L. (1993). J. Mol. Biol. 234, 779-815.
34. Sheriff, S., Klei, H. E. & Davis, M. E. (1999). J. Appl. Cryst. 32, 98-101.
35. Shortle, D., Simons, K. T. & Baker, D. (1998). Proc. Natl Acad. Sci. USA, 95, 11158-11162.
36. Thumiger, A. (2008). PhD Thesis in Molecular Sciences. University of Padua. http://paduaresearch.cab.unipd.it/979/1/Thumiger-thesis.pdf. Wilson, A. J. C. (1942). Nature (London), 150, 150-152.
37. Zhang, Y. (2008). BMC Bioinformatics, 9, 40.