PDB_REDO: automated re-refinement of X-ray structure models in the PDB
- ️Vriend, G.
- ️Fri Apr 03 2009
References
Adams, P. (2009). Personal communication. Google Scholar
Beernink, P., Endrizzi, J., Alber, T. & Schachman, H. (2009). In preparation. Google Scholar
Berman, H. M., Henrick, K. & Nakamura, H. (2003). Nat. Struct. Biol. 10, 980. Web of Science CrossRef PubMed Google Scholar
Berman, H. M., Henrick, K., Nakamura, H. & Markley, J. L. (2007). Nucleic Acids Res. 35, 301–333. Web of Science CrossRef Google Scholar
Bricogne, G. (1997). Methods Enzymol. 276, 361–423. CrossRef CAS Web of Science Google Scholar
Brünger, A. T. (1992). Nature (London), 355, 472–475. PubMed Web of Science Google Scholar
Chang, G., Roth, C. B., Reyes, C. L., Pornillos, O., Chen, Y. J. & Chen, A. P. (2006). Science, 314, 1875. CrossRef PubMed Google Scholar
Collaborative Computational Project, Number 4 (1994). Acta Cryst. D50, 760–763. CrossRef IUCr Journals Google Scholar
Engh, R. A. & Huber, R. (1991). Acta Cryst. A47, 392–400. CrossRef CAS Web of Science IUCr Journals Google Scholar
French, S. & Wilson, K. (1978). Acta Cryst. A34, 517–525. CrossRef CAS IUCr Journals Web of Science Google Scholar
Henrick, K. et al. (2008). Nucleic Acids Res. 36, D426–D433. Web of Science CrossRef PubMed CAS Google Scholar
Hooft, R. W. W., Sander, C. & Vriend, G. (1997). CABIOS, 13, 425–430. CAS PubMed Web of Science Google Scholar
Hooft, R. W. W., Vriend, G., Sander, C. & Abola, E. E. (1996). Nature (London), 381, 272. CrossRef PubMed Web of Science Google Scholar
Hub, J. S., Salditt, T., Rheinstädter, M. C. & de Groot, B. L. (2007). Biophys. J. 93, 3156–3168. Web of Science CrossRef PubMed CAS Google Scholar
Jacq, N. et al. (2007). Parallel Comput. 33, 289–301. Web of Science CrossRef Google Scholar
Joosten, R. P., Chinea, G., Kleywegt, G. J. & Vriend, G. (2007). Comprehensive Medical Chemistry II, Vol. 3, edited by H. Kubinyi, pp. 507–530. Oxford: Elsevier. Google Scholar
Joosten, R. P., Womack, T., Vriend, G. & Bricogne, G. (2009). Acta Cryst. D65, 176–185. Web of Science CrossRef CAS IUCr Journals Google Scholar
Karplus, P. A. (1996). Protein Sci. 5, 1406–1420. CrossRef CAS PubMed Web of Science Google Scholar
Kleywegt, G. J., Harris, M. R., Zou, J., Taylor, T. C., Wählby, A. & Jones, T. A. (2004). Acta Cryst. D60, 2240–2249. Web of Science CrossRef CAS IUCr Journals Google Scholar
Kleywegt, G. J. & Jones, T. A. (1995). Structure, 3, 535–540. CrossRef CAS PubMed Web of Science Google Scholar
Kleywegt, G. J. & Jones, T. A. (2002). Structure, 10, 465–472. Web of Science CrossRef PubMed CAS Google Scholar
Krieger, E., Darden, T., Nabuurs, S. B., Finkelstein, A. & Vriend, G. (2004). Proteins, 57, 678–683. Web of Science CrossRef PubMed CAS Google Scholar
Laskowski, R. A., Chistyakov, V. V. & Thornton, J. M. (2005). Nucleic Acids Res. 33, 266–268. Web of Science CrossRef Google Scholar
Laskowski, R. A., MacArthur, M. W., Moss, D. S. & Thornton, J. M. (1993). J. Appl. Cryst. 26, 283–291. CrossRef CAS Web of Science IUCr Journals Google Scholar
Lee, H.-C., Salzemann, J., Jacq, N., Chen, H.-Y., Ho, L.-Y., Merelli, I., Milanesi, L., Breton, V., Lin, S. C. & Wu, Y.-T. (2006). IEEE Trans. Nanobiosci. 6, 288–295. Web of Science CrossRef Google Scholar
Lütteke, T. & von der Lieth, C. W. (2004). BMC Bioinformatics, 5, 69. Google Scholar
McCarthy, A. A., Walsh, M. A., Verma, C. S., O'Connell, D. P., Reinhold, M., Yalloway, G. N., D'Arcy, D., Higgins, T. M., Voordouw, G. & Mayhew, S. G. (2002). Biochemistry, 41, 10950–10962. Web of Science CrossRef PubMed CAS Google Scholar
Morris, R. J., Perrakis, A. & Lamzin, V. S. (2007). Macromolecular Crystallography – Conventional and High-throughput Methods, edited by M. R. Sanderson & J. V. Skelly, pp. 155–172. Oxford University Press. Google Scholar
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. Web of Science CrossRef PubMed CAS Google Scholar
Nabuurs, S. B., Wagener, M. & de Vlieg, J. (2007). J. Med. Chem. 50, 6507–6518. Web of Science CrossRef PubMed CAS Google Scholar
Nederveen, A. J., Doreleijers, J. F., Vranken, W., Miller, Z., Spronk, C. A. E. M., Nabuurs, S. B., Güntert, P., Livny, M., Markley, J. L., Nilges, M., Ulrich, E. L., Kaptein, R. & Bonvin, A. M. J. J. (2005). Proteins, 59, 662–672. Web of Science CrossRef PubMed CAS Google Scholar
Painter, J. & Merritt, E. A. (2006). Acta Cryst. D62, 439–450. Web of Science CrossRef CAS IUCr Journals Google Scholar
Pantoliano, M. W., Whitlow, M., Wood, J. F., Dodd, S. W., Hardman, K. D., Rollence, M. L. & Bryan, P. N. (1989). Biochemistry, 28, 7205–7213. CrossRef CAS PubMed Web of Science Google Scholar
Rajashankar, K. R., Ray, S. S., Bonanno, J. B., Pinho, M. G., He, G., De Lencastre, H., Tomasz, A. & Burley, S. K. (2002). Structure, 10, 1499–1508. Web of Science PubMed Google Scholar
Schomaker, V. & Trueblood, K. N. (1968). Acta Cryst. B24, 63–76. CrossRef CAS IUCr Journals Web of Science Google Scholar
Sheldrick, G. M. (1990). Acta Cryst. A46, 467–473. CrossRef CAS Web of Science IUCr Journals Google Scholar
Sheldrick, G. M. & Schneider, T. R. (1997). Methods Enzymol. 277, 319–343. CrossRef PubMed CAS Web of Science Google Scholar
Smart, O. S., Brandl, M., Flensburg, C., Keller, P., Paciorek, W., Vonrhein, C., Womack, T. O. & Bricogne, G. (2008). Abstracts of the Annual Meeting of the American Crystallographic Association, Knoxville, Tennessee, USA. Google Scholar
Smith, R. D. (1999). PhD thesis, Rice University, USA. Google Scholar
Stockinger, H., Pagni, M., Cerutti, L. & Falquet, L. (2006). 2nd IEEE International Conference on e-Science and Grid Computing (e-Science 2006), pp. 58–65. Amsterdam: IEEE Computer Society Press. Google Scholar
Tickle, I. J. (2007). Acta Cryst. D63, 1274–1281. Web of Science CrossRef CAS IUCr Journals Google Scholar
Tickle, I. J., Laskowski, R. A. & Moss, D. S. (1998). Acta Cryst. D54, 547–557. Web of Science CrossRef CAS IUCr Journals Google Scholar
Tronrud, D. E. (2008). Abstracts of the Annual Meeting of the American Crystallographic Association, Knoxville, Tennessee, USA, and personal communication. Google Scholar
Winn, M. D., Isupov, M. N. & Murshudov, G. N. (2001). Acta Cryst. D57, 122–133. Web of Science CrossRef CAS IUCr Journals Google Scholar
This is an open-access article distributed under the terms of the Creative Commons Attribution (CC-BY) Licence, which permits unrestricted use, distribution, and reproduction in any medium, provided the original authors and source are cited.