Automated crystallographic ligand building using the medial axis transform of an electron-density isosurface

Acta Crystallographica Section D: Biological Crystallography

Volumn 61, Issue 10, 2005, Pages 1354-1363

  Aishima, Jun ^a,b   Russel, Daniel S ^c   Guibas, Leonidas J ^c   Adams, Paul D ^d   Brunger, Axel T ^a,b  

^a SLAC NATIONAL ACCELERATOR LABORATORY   (United States)

^b HOWARD HUGHES MEDICAL INSTITUTE   (United States)

^c Stanford University   (United States)

^d LAWRENCE BERKELEY NATIONAL LABORATORY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

LIGAND; PROTEIN;

ALGORITHM; ARTICLE; AUTOMATED PATTERN RECOGNITION; AUTOMATION; CHEMICAL STRUCTURE; CHEMISTRY; CONFORMATION; ELECTRON; MACROMOLECULE; METHODOLOGY; PROTEIN CONFORMATION; STATISTICAL MODEL; X RAY CRYSTALLOGRAPHY;

ALGORITHMS; AUTOMATION; CRYSTALLOGRAPHY, X-RAY; ELECTRONS; LIGANDS; MACROMOLECULAR SUBSTANCES; MODELS, MOLECULAR; MODELS, STATISTICAL; MOLECULAR CONFORMATION; PATTERN RECOGNITION, AUTOMATED; PROTEIN CONFORMATION; PROTEINS;

EID: 32944458334     PISSN: 09074449     EISSN: 13990047     Source Type: Journal    
DOI: 10.1107/S0907444905023152     Document Type: Article

References (46)

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. Adolph, H. W., Zwart, P., Meijers, R., Hubatsch, I., Kiefer, M., Lamzin, V. & Cedergren-Zeppezauer, E. (2000). Biochemistry, 39, 12885-12897.
3. Agarwal, R. C. (1978). Acta Cryst. A34, 791-809.
4. Amenta, N., Choi, S., Dey, T. K. & Leekha, N. (2002). Int. J. Comput. Geom. Appl. 12, 125-141.
5. Amenta, N., Choi, S., Jump, M. E., Kolluri, R. & Wahl, T. (2002). Report TR-02-27. University of Texas at Austin, USA.
6. Amenta, N., Choi, S. & Kolluri, R. (2001). Sixth ACM Symposium on Solid Modeling and Applications, June 4-8, 2001, pp. 249-260. Ann Arbor, MI, USA: ACM Press.
7. Antonyuk, S. V., Grebenko, A. I., Levdikov, V. M., Urusova, D. V., Melik-Adamyan, W. R., Lamzin, V. S. & Wilson, K. S. (2001). Kristallogrofiya, 46, 687-691.
8. Bell, I. M. et al. (2002). J. Med. Chem. 45, 2388-2409.
9. Blum, H. (1967). Models for the Perception of Speech and Visual Form, edited by W. Whaten-Dunn, pp. 362-380. Cambridge, MA, USA: MIT Press.
10. 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.
11. Card, G. L., Blasdel, L., England, B. P., Zhang, C., Suzuki, Y., Gillette, S., Fong, D., Ibrahim, P. N., Artis, D. R., Bollag, G., Milburn, M. V., Kim, S. H., Schlessinger, J. & Zhang, K. Y. (2005). Nature Biotechnol. 23, 201-207.
12. Collaborative Computational Project, Number 4 (1994). Acta Cryst. D50, 760-763.
13. Cowtan, K. (1998). Acta Cryst. D54, 750-756.
14. DeLano, W. L. (2002). The PyMOL Molecular Graphics System. http://www.pymol.org.
15. Fortier, S., Chiverton, A., Glasgow, J. & Leherte, L. (1997). Methods Enzymol. 277, 131-157.
16. Greer, J. (1985). Methods Enzymol. 115, 206-224.
17. Grochulski, P., Bouthillier, F., Kazlauskas, R. J., Serreqi, A. N., Schrag, J. D., Ziomek, E. & Cygler, M. (1994). Biochemistry, 33, 3494-3500.
18. Grosse-Kunstleve, R. W., Sauter, N. K., Moriarty, N. W. & Adams, P. D. (2002). J. Appl. Cryst. 35, 126-136.
19. Han, G. W., Lee, J. Y., Song, H. K., Chang, C., Min, K., Moon, J., Shin, D. H., Kopka, M. L., Sawaya, M. R., Yuan, H. S., Kim, T. D., Choe, J., Lim, D., Moon, H. J. & Suh, S. W. (2001). J. Mol. Biol. 308, 263-278.
20. Kearsley, S. K. (1989). Acta Cryst. A45, 208-210.
21. Kleywegt, G. J. (1996). Acta Cryst. D52, 826-828.
22. Kleywegt, G. J., Bergfors, T., Senn, H., Le Motte, P., Gsell, B., Shudo, K. & Jones, T. A. (1994). Structure, 2, 1241-1258.
23. Kleywegt, G. J. & Jones, T. A. (1997). Acta Cryst. D53, 179-185.
24. Kleywegt, G. J. & Jones, T. A. (1998). Acta Cryst. D54, 1119-1131.
25. Korostelev, A., Bertram, R. & Chapman, M. S. (2002). Acta Cryst. D58, 761-767.
26. Lamzin, V. S., Perrakis, A. & Wilson, K. S. (2001). International Tables for Crystallography, Vol. F, edited by M. G. Rossmann & E. Arnold, pp. 720-722. Dordrecht: Kluwer Academic Publishers.
27. Lascombe, M. B., Ponchet, M., Venard, P., Milat, M. L., Blein, J. P. & Prangé, T. (2002). Acta Cryst. D58, 1442-1447.
28. Leherte, L., Glasgow, J., Baxter, K., Steeg, E. & Fortier, S. (1997). J. Artif. Intell. Res. 7, 125-159.
29. Levitt, D. G. (2001). Acta Cryst. D57, 1013-1019.
30. Lorentzen, E., Pohl, E., Zwart, P., Stark, A., Russell, R. B., Knura, T., Hensel, R. & Siebers, B. (2003). J. Biol. Chem. 278, 47253-47260.
31. Morollo, A. A. & Eck, M. J. (2001). Nature Struct. Biol. 8, 243-247.
32. Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255.
33. Nunn, C. M. & Neidle, S. (1995). J. Med. Chem. 38, 2317-2325.
34. Oldfield, T. J. (2001). Acta Cryst. D57, 696-705.
35. Paik, D. S., Beaulieu, C. F., Jeffrey, R. B., Rubin, G. D. & Napel, S. (1998). Med. Phys. 25, 629-637.
36. Pitt, W. R., Williams, M. A., Steven, M., Sweeney, B., Bleasby, A. J. & Moss, D. S. (2001). Bioinformatics, 17, 729-737.
37. Potterton, E., Briggs, P., Turkenburg, M. & Dodson, E. (2003). Acta Cryst. D59, 1131-1137.
38. Sawaya, M. R. & Kraut, J. (1997). Biochemistry, 36, 586-603.
39. Selinsky, B. S., Gupta, K., Sharkey, C. T. & Loll, P. J. (2001). Biochemistry, 40, 5172-5180.
40. Siek, J. G., Lee, L.-Q. & Lumsdaine, A. (2002). The Boost Graph Library: User Guide and Reference Manual. New York: Addison-Wesley.
41. Swanson, S. M. (1994). Acta Cryst. D50, 695-708.
42. Terwilliger, T. C. (2002). Acta Cryst. D58, 1937-1940.
43. Wang, C. E. (2000). Acta Cryst. D56, 1591-1611.
44. Williams, S. P. & Sigler, P. B. (1998). Nature (London), 393, 392-396.
45. Zhang, K. Y., Card, G. L., Suzuki, Y., Artis, D. R., Fong, D., Gillette, S., Hsieh, D., Neiman, J., West, B. L., Zhang, C., Milburn, M. V., Kim, S.-H., Schlessinger, J. & Bollag, G. (2004). Mol. Cell, 15, 279-286.
46. Zwart, P. H., Langer, G. G. & Lamzin, V. S. (2004). Acta Cryst. D60, 2230-2239.