Validation of ligands in macromolecular structures determined by X-ray crystallography

Acta Crystallographica Section D: Structural Biology

Volumn 74, Issue , 2018, Pages 228-236

  Smart, Oliver S ^a   Horský, Vladimír ^b   Gore, Swanand ^a   Vařeková, Radka Svobodová ^b   Bendová, Veronika ^b   Kleywegt, Gerard J ^a   Velankar, Sameer ^a  

^a EUROPEAN BIOINFORMATICS INSTITUTE   (United Kingdom)

^b MASARYK UNIVERSITY   (Czech Republic)

Author keywords

ligands; PDB; Protein Data Bank; three dimensional macromolecular structure; validation

Indexed keywords

LIGAND; PROTEIN;

CHEMICAL STRUCTURE; CHEMISTRY; HUMAN; MACROMOLECULE; MOLECULAR MODEL; PROTEIN CONFORMATION; PROTEIN DATABASE; VALIDATION STUDY; X RAY CRYSTALLOGRAPHY;

CRYSTALLOGRAPHY, X-RAY; DATABASES, PROTEIN; HUMANS; LIGANDS; MACROMOLECULAR SUBSTANCES; MODELS, MOLECULAR; MOLECULAR STRUCTURE; PROTEIN CONFORMATION; PROTEINS;

EID: 85043764737     PISSN: None     EISSN: 20597983     Source Type: Journal    
DOI: 10.1107/S2059798318002541     Document Type: Article

References (57)

1. Adams, P. D. et al. (2016). Structure, 24, 502-508.
2. Akker, F. van den & Hol, W. G. J. (1999). Acta Cryst. D55, 206-218.
3. Bell, J. A., Ho, K. L. & Farid, R. (2012). Acta Cryst. D68, 935-952.
4. Berkholz, D. S., Faber, H. R., Savvides, S. N. & Karplus, P. A. (2008). J. Mol. Biol. 382, 371-384.
5. Berman, H. M., Kleywegt, G. J., Nakamura, H. & Markley, J. L. (2013). Structure, 21, 1485-1491.
6. Beshnova, D. A., Pereira, J. & Lamzin, V. S. (2017). Acta Cryst. D73, 195-202.
7. Borbulevych, O. Y., Plumley, J. A., Martin, R. I., Merz, K. M. & Westerhoff, L. M. (2014). Acta Cryst. D70, 1233-1247.
8. Bruno, I. J., Cole, J. C., Kessler, M., Luo, J., Motherwell, W. D. S., Purkis, L. H., Smith, B. R., Taylor, R., Cooper, R. I., Harris, S. E. & Orpen, A. G. (2004). J. Chem. Inf. Comput. Sci. 44, 2133-2144.
9. Bruno, I. J., Cole, J. C., Lommerse, J. P. M., Rowland, R. S., Taylor, R. & Verdonk, M. L. (1997). J. Comput. Aided Mol. Des. 11, 525-537.
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. Davis, A. M., Stgallay, S. & Kleywegt, G. J. (2008). Drug Discov. Today, 13, 831-841.
12. Deller, M. C. & Rupp, B. (2015). J. Comput. Aided Mol. Des. 29, 817-836.
13. Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. (2010). Acta Cryst. D66, 486-501.
14. Engh, R. A. & Huber, R. (2001). International Tables for Crystallography, Vol. F, edited by M. G. Rossmann & E. Arnold, pp. 382-392. Dordrecht: Kluwer Academic Publishers.
15. Global Phasing Ltd (2011). BUSTER-Report. https:// www.globalphasing.com/BUSTER/wiki/index.cgi?BusterReport.
16. Gore, S. et al. (2017). Structure, 25, 1916-1927.
17. Gore, S., Velankar, S. & Kleywegt, G. J. (2012). Acta Cryst. D68, 478-483.
18. He, X., Alian, A., Stroud, R. & Ortiz de Montellano, P. R. (2006). J. Med. Chem. 49, 6308-6323.
19. Huey, R., Morris, G. M., Olson, A. J. & Goodsell, D. S. (2007). J. Comput. Chem. 28, 1145-1152.
20. Janowski, P. A., Moriarty, N.W., Kelley, B. P., Case, D. A., York, D. M., Adams, P. D. & Warren, G. L. (2016). Acta Cryst. D72, 1062-1072.
21. Jones, T. A., Zou, J.-Y., Cowan, S. W. & Kjeldgaard, M. (1991). Acta Cryst. A47, 110-119.
22. Kleywegt, G. J. (2000). Acta Cryst. D56, 249-265.
23. Kleywegt, G. J. (2007). Acta Cryst. D63, 94-100.
24. Kleywegt, G. J., Harris, M. R., Zou, J., Taylor, T. C., Wählby, A. & Jones, T. A. (2004). Acta Cryst. D60, 2240-2249.
25. Kleywegt, G. J., Henrick, K., Dodson, E. J. & van Aalten, D. M. F. (2003). Structure, 11, 1051-1059.
26. Kleywegt, G. J. & Jones, T. A. (1995). Structure, 3, 535-540.
27. Kleywegt, G. J. & Jones, T. A. (1998). Acta Cryst. D54, 1119-1131.
28. Kleywegt, G. J. & Jones, T. A. (2002). Structure, 10, 465-472.
29. Liebeschuetz, J., Hennemann, J., Olsson, T. & Groom, C. R. (2012). J. Comput. Aided Mol. Des. 26, 169-183.
30. Macrae, C. F., Bruno, I. J., Chisholm, J. A., Edgington, P. R., McCabe, P., Pidcock, E., Rodriguez-Monge, L., Taylor, R., van de Streek, J. & Wood, P. A. (2008). J. Appl. Cryst. 41, 466-470.
31. Meyder, A., Nittinger, E., Lange, G., Klein, R. & Rarey, M. (2017). J. Chem. Inf. Model. 57, 2437-2447.
32. Mir, S. et al. (2018). Nucleic Acids Res. 46, D486-D492.
33. Mir, R., Singh, N., Vikram, G., Kumar, R. P., Sinha, M., Bhushan, A., Kaur, P., Srinivasan, A., Sharma, S. & Singh, T. P. (2009). Biophys. J. 97, 3178-3186.
34. Moriarty, N.W., Grosse-Kunstleve, R.W. & Adams, P. D. (2009). Acta Cryst. D65, 1074-1080.
35. Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S. & Olson, A. J. (2009). J. Comput. Chem. 30, 2785-2791.
36. Murshudov, G. N., Skubák, 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.
37. Naschberger, A., Fürnrohr, B. G., Lenac Rovis, T., Malic, S., Scheffzek, K., Dieplinger, H. & Rupp, B. (2016). Acta Cryst. D72, 1267-1280.
38. Parkinson, G., Vojtechovsky, J., Clowney, L., Brünger, A. T. & Berman, H. M. (1996). Acta Cryst. D52, 57-64.
39. Pearce, N. M., Krojer, T., Bradley, A. R., Collins, P., Nowak, R. P., Talon, R., Marsden, B. D., Kelm, S., Shi, J., Deane, C. M. & von Delft, F. (2017). Nature Commun. 8, 15123.
40. Pozharski, E., Weichenberger, C. X. & Rupp, B. (2013). Acta Cryst. D69, 150-167.
41. Ramachandran, G. N., Ramakrishnan, C. & Sasisekharan, V. (1963). J. Mol. Biol. 7, 95-99.
42. Read, R. J. et al. (2011). Structure, 19, 1395-1412.
43. Rupp, B. (2010). Biomolecular Crystallography: Principles, Practice, and Application to Structural Biology. New York: Garland Science.
44. Scapin, G., Patel, D. & Arnold, E. (2015). Multifaceted Roles of Crystallography in Modern Drug Discovery. Dordrecht: Springer.
45. Sehnal, D., Deshpande,M., Vařeková, R. S., Mir, S., Berka, K.,Midlik, A., Pravda, L., Velankar, S. & Koča, J. (2017). Nature Methods, 14, 1121-1122.
46. Shen, H. (2014). Nature (London), 515, 151-152.
47. Shimizu, T., Nakatsu, T., Miyairi, K., Okuno, T. & Kato, H. (2002). Biochemistry, 41, 6651-6659.
48. Smart, O. S. & Bricogne, G. (2015). Multifaceted Roles of Crystallography in Modern Drug Discovery, edited by G. Scapin, D. Patel & E. Arnold, pp. 165-181. Dordrecht: Springer. https://doi.org/ 10.1007/978-94-017-9719-1-13.
49. Smart, O. S., Liebeschuetz, J. W., Sharff, A., Flensburg, C., Keller, P., Paciorek, W. & Bricogne, G. (2016). Assessing Ligand Strain Energy in BUSTER Protein-Complex Structure Refinement. https://eventbooking.stfc.ac.uk/uploads/ccp4-study-weekend-2016/assessing-ligand-strain-energy-in-buster-protein-complex-structurerefinement---oliver-smart.pdf.
50. Smart, O. S., Womack, T. O., Flensburg, C., Keller, P., Paciorek, W., Sharff, A., Vonrhein, C. & Bricogne, G. (2012). Acta Cryst. D68, 368-380.
51. Stierand, K. & Rarey, M. (2010). ACS Med. Chem. Lett. 1, 540-545.
52. Tickle, I. J. (2012). Acta Cryst. D68, 454-467.
53. Wallace, A. C., Laskowski, R. A. & Thornton, J. M. (1995). Protein Eng. 8, 127-134.
54. Warren, G. L., Do, T. D., Kelley, B. P., Nicholls, A. & Warren, S. D. (2012). Drug Discov. Today, 17, 1270-1281.
55. Winn, M. D. et al. (2011). Acta Cryst. D67, 235-242.
56. wwPDB (2016). User Guide to the wwPDB X-ray Validation Reports. https://www.wwpdb.org/validation/2016/XrayValidationReportHelp.
57. Zubieta, C., Kota, P., Ferrer, J.-L., Dixon, R. A. & Noel, J. P. (2002). Plant Cell, 14, 1265-1277.