Accurate macromolecular crystallographic refinement: Incorporation of the linear scaling, semiempirical quantum-mechanics program DivCon into the PHENIX refinement package

Acta Crystallographica Section D: Biological Crystallography

Volumn 70, Issue 5, 2014, Pages 1233-1247

  Borbulevych, Oleg Y ^a   Plumley, Joshua A ^a   Martin, Roger I ^a   Merz, Kenneth M ^b   Westerhoff, Lance M ^a  

^a QUANTUMBIO INC   (United States)

^b UNIVERSITY OF FLORIDA   (United States)

Author keywords

high throughput crystallography; ligand strain; quantum mechanics refinement; regional refinement; stereochemical restraints; X ray crystallography

Indexed keywords

LIGAND; MACROMOLECULE; PROTEIN;

CHEMICAL STRUCTURE; CHEMISTRY; FACTUAL DATABASE; HIGH THROUGHPUT SCREENING; IMAGE PROCESSING; MACROMOLECULE; PROTEIN DATABASE; QUANTUM THEORY; REPRODUCIBILITY; SOFTWARE; STEREOISOMERISM; X RAY CRYSTALLOGRAPHY;

CRYSTALLOGRAPHY, X-RAY; DATABASES, FACTUAL; DATABASES, PROTEIN; HIGH-THROUGHPUT SCREENING ASSAYS; IMAGE PROCESSING, COMPUTER-ASSISTED; LIGANDS; MACROMOLECULAR SUBSTANCES; MODELS, MOLECULAR; PROTEINS; QUANTUM THEORY; REPRODUCIBILITY OF RESULTS; SOFTWARE; STEREOISOMERISM;

EID: 84900395603     PISSN: 09074449     EISSN: 13990047     Source Type: Journal    
DOI: 10.1107/S1399004714002260     Document Type: Article

References (65)

1. Adams, P. D. et al. (2010). Acta Cryst. D66, 213-221.
2. Afonine, P. V., Grosse-Kunstleve, R. W., Echols, N., Headd, J. J., Moriarty, N. W., Mustyakimov, M., Terwilliger, T. C., Urzhumtsev, A., Zwart, P. H. & Adams, P. D. (2012). Acta Cryst. D68, 352-367.
3. Allen, F. H., Kennard, O., Watson, D. G., Brammer, L., Orpen, A. G. & Taylor, R. (1987). J. Chem. Soc. Perkin Trans. 2, pp. S1-S19.
4. Borbulevych, O., Merz Jr, K. M. & Westerhoff, L. M. (2011). Acta Cryst. A67, C593.
5. Borbulevych, O. Y., Plumley, J. A. & Westerhoff, L. M. (2012). Abstr. Pap. Am. Chem. Soc., abstract 478.
6. Borbulevych, O. & Westerhoff, L. M. (2011). Abstr. Pap. Am. Chem. Soc., abstract 242.
7. Brü nger, 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.
8. Brünger, A. T. & Rice L. M.(1997). Methods Enzymol. 277:243-269.
9. Case, D. A. et al. (2010). AMBER 11. University of California, San Francisco, USA.
10. Chen, V. B., Arendall, W. B., Headd, J. J., Keedy, D. A., Immormino, R. M., Kapral, G. J., Murray, L. W., Richardson, J. S. & Richardson, D. C. (2010). Acta Cryst. D66, 12-21.
11. Chen, Y. T., Brinen, L. S., Kerr, I. D., Hansell, E., Doyle, P. S., McKerrow, J. H. & Roush, W. R. (2010). PLoS Negl. Trop. Dis. 4, e825.
12. Cooper, D. R., Porebski, P. J., Chruszcz, M. & Minor, W. (2011). Expert Opin. Drug Discov. 6, 771-782.
13. Cozier, G. E., Leese, M. P., Lloyd, M. D., Baker, M. D., Thiyagarajan, N., Acharya, K. R. & Potter, B. V. L. (2010). Biochemistry, 49, 3464-3476.
14. Davis, I. W., Leaver-Fay, A., Chen, V. B., Block, J. N., Kapral, G. J., Wang, X., Murray, L. W., Arendall, W. B., Snoeyink, J., Richardson, J. S. & Richardson, D. C. (2007). Nucleic Acids Res. 35, W375-W383.
15. Dewar, M. J. S., Zoebisch, E. G., Healy, E. F. & Stewart, J. J. P. (1985). J. Am. Chem. Soc. 107, 3902-3909.
16. Diller, D. J., Humblet, C., Zhang, X. & Westerhoff, L. M. (2010). Proteins, 78, 2329-2337.
17. Dixon, S. L. & Merz, K. M. Jr (1996). J. Chem. Phys. 104, 6643.
18. Dixon, S. L. & Merz, K. M. Jr (1997). J. Chem. Phys. 107, 879.
19. Dixon, S., Merz, K. M. Jr, Lauri, G. & Ianni, J. C. (2005). J. Comput. Chem. 26, 23-34.
20. Dodson, E., Kleywegt, G. J. & Wilson, K. (1996). Acta Cryst. D52, 228-234.
21. Engh, R. A. & Huber, R. (1991). Acta Cryst. A47, 392-400.
22. Evans, P. R. (2007). Acta Cryst. D63, 58-61.
23. Fu, Z., Li, X. & Merz, K. M. Jr (2011). J. Comput. Chem. 32, 2587-2597.
24. Fu, Z., Li, X. & Merz, K. M. Jr (2012). J. Chem. Theory Comput. 8, 1436-1448.
25. Gore, S., Olsson, T. S. G. & Zhuravleva, M. (2011). Acta Cryst. A67, C104.
26. Harding, M. M. (1999). Acta Cryst. D55, 1432-1443.
27. Hostas, J., Rezác, J. & Hobza, P. (2013). Chem. Phys. Lett. 568-569, 161-166.
28. Jaskolski, M., Gilski, M., Dauter, Z. & Wlodawer, A. (2007). Acta Cryst. D63, 611-620.
29. Joosten, R. P., Joosten, K., Murshudov, G. N. & Perrakis, A. (2012). Acta Cryst. D68, 484-496.
30. Kleywegt, G. J. (2007). Acta Cryst. D63, 94-100.
31. Kleywegt, G. J. & Jones, T. A. (1996). Structure, 4, 1395-1400.
32. Korth, M., Pitonák, M., Rezác, J. & Hobza, P. (2010). J. Chem. Theory Comput. 6, 344-352.
33. Labute, P. (2005). J. Chem. Inf. Model. 45, 215-221.
34. Lack, N. A., Yam, K. C., Lowe, E. D., Horsman, G. P., Owen, R. L., Sim, E. & Eltis, L. D. (2010). J. Biol. Chem. 285, 434-443.
35. Lascombe, M.-B., Ponchet, M., Venard, P., Milat, M.-L., Blein, J.-P. & Prangé, T. (2002). Acta Cryst. D58, 1442-1447.
36. Laskowski, R. A., MacArthur, M. W., Moss, D. S. & Thornton, J. M. (1993). J. Appl. Cryst. 26, 283-291.
37. Li, X., Hayik, S. A. & Merz, K. M. Jr (2010). J. Inorg. Biochem. 104, 512-522.
38. Liebeschuetz, J., Hennemann, J., Olsson, T. & Groom, C. R. (2012). J. Comput. Aided Mol. Des. 26, 169-183.
39. Liu, D. C. & Nocedal, J. (1989). Math. Program. 45, 503-528.
40. Merritt, E. A. (2012). Acta Cryst. D68, 468-477.
41. Merz, K. M. Jr & Raha, K. (2011). US Patent 7904283.
42. Moriarty, N.W., Grosse-Kunstleve, R.W. & Adams, P. D. (2009). Acta Cryst. D65, 1074-1080.
43. Murshudov, G. N., Skubá k, P., Lebedev, A. A., Pannu, N. S., Steiner, R. A., Nicholls, R. A., Winn, M. D., Long, F. & Vagin, A. A. (2011). Acta Cryst. D67, 355-367.
44. Murshudov, G. N., Vagin, A. A. & Dodson, E. J. (1997). Acta Cryst. D53, 240-255.
45. Perola, E. & Charifson, P. S. (2004). J. Med. Chem. 47, 2499-2510.
46. Peters, M. B. & Merz, K. M. Jr (2006). J. Chem. Theory Comput. 2, 383-399.
47. Pozharski, E., Weichenberger, C. X. & Rupp, B. (2013). Acta Cryst. D69, 150-167.
48. Raha, K. & Merz, K. M. Jr (2004). J. Am. Chem. Soc. 126, 1020-1021.
49. Raha, K. & Merz, K. M. Jr (2005). J. Med. Chem. 48, 4558-4575.
50. Rezac, J., Fanfrlk, J., Salahub, D. & Hobza, P. (2009). J. Chem. Theory Comput. 5, 1749-1760.
51. Schmidt, M. W., Baldridge, K. K., Boatz, J. A., Elbert, S. T., Gordon, M. S., Jensen, J. H., Koseki, S., Matsunaga, N., Nguyen, K. A., Su, S., Windus, T. L., Dupuis, M. & Montgomery, J. A. (1993). J. Comput. Chem. 14, 1347-1363.
52. Shimizu, M., Miyamoto, Y., Takaku, H., Matsuo, M., Nakabayashi, M., Masuno, H., Udagawa, N., DeLuca, H. F., Ikura, T. & Ito, N. (2008). Bioorg. Med. Chem. 16, 6949-6964.
53. Smart, O. S., Womack, T. O., Flensburg, C., Keller, P., Paciorek, W., Sharff, A., Vonrhein, C. & Bricogne, G. (2011). Acta Cryst. A67, C134.
54. Stewart, J. J. P. (2009). J. Mol. Model. 15, 765-805.
55. Stewart, J. J. P. (2013). J. Mol. Model. 19, 1-32.
56. Terwilliger, T. C., Klei, H., Adams, P. D., Moriarty, N.W. & Cohn, J. D. (2006). Acta Cryst. D62, 915-922.
57. Tronrud, D. E. (2004). Acta Cryst. D60, 2156-2168.
58. Vaart, A. van der, Gogonea, V., Dixon, S. L. & Merz, K. M. Jr (2000). J. Comput. Chem. 21, 1494-1504.
59. Vaart, A. van der., Suarez, D. & Merz, K. M. Jr (2000). J. Chem. Phys. 113, 10512-10523.
60. Wang, B., Raha, K. & Merz, K. M. Jr (2004). J. Am. Chem. Soc. 126, 11430-11431.
61. Wang, B., Westerhoff, L. M. & Merz, K. M. Jr (2007). J. Med. Chem. 50, 5128-5134.
62. Williams, D. E., Peters, M. B., Wang, B., Roitberg, A. E. & Merz, K. M. Jr (2009). J. Phys. Chem. A, 113, 11550-11559.
63. Wlodek, S., Skillman, A. G. & Nicholls, A. (2006). Acta Cryst. D62, 741-749.
64. Yu, N., Yennawar, H. P. & Merz, K. M. Jr (2005). Acta Cryst. D61, 322-332.
65. Zhang, X., Gibbs, A. C., Reynolds, C. H., Peters, M. B. & Westerhoff, L. M. (2010). J. Chem. Inf. Model. 50, 651-661.