Realising the importance of assessing the quality of the biomolecular structures deposited in the Protein Data Bank (PDB), the Worldwide Protein Data Bank (wwPDB) partners established Validation Task Forces to obtain advice on the methods and standards to be used to validate structures determined by X-ray crystallography, nuclear magnetic resonance spectroscopy and three-dimensional electron cryo-microscopy. The resulting wwPDB validation pipeline is an integral part of the wwPDB OneDep deposition, biocuration and validation system. The wwPDB Validation Service webserver (https://validate.wwpdb.org) can be used to perform checks prior to deposition. Here, it is shown how validation metrics can be combined to produce an overall score that allows the ranking of macromolecular structures and domains in search results. The ValTrendsDB database provides users with a convenient way to access and analyse validation information and other properties of X-ray crystal structures in the PDB, including investigating trends in and correlations between different structure properties and validation metrics.

CEITEC Central European Institute of Technology Masaryk University Kamenice 5 625 00 Brno Czech Republic

Faculty of Science National Centre for Biomolecular Research Kamenice 5 625 00 Brno Czech Republic

Protein Data Bank in Europe European Molecular Biology Laboratory European Bioinformatics Institute Wellcome Genome Campus Hinxton Cambridge CB10 1SD England

Zobrazit více v PubMed

Agirre, J., Iglesias-Fernández, J., Rovira, C., Davies, G. J., Wilson, K. S. & Cowtan, K. D. (2015). Nature Struct. Mol. Biol. 22, 833–834. PubMed

Berman, H., Henrick, K. & Nakamura, H. (2003). Nature Struct. Biol. 10, 980. PubMed

Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. N. & Bourne, P. E. (2000). Nucleic Acids Res. 28, 235–242. PubMed PMC

Bousfield, D., McEntyre, J., Velankar, S., Papadatos, G., Bateman, A., Cochrane, G., Kim, J.-H., Graef, F., Vartak, V., Alako, B. & Blomberg, N. (2016). F1000Res. 5, ELIXIR-160. PubMed PMC

Brünger, A. T. (1992). Nature (London), 355, 472–475. PubMed

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. PubMed

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. PubMed

Buckley, D. L., Gustafson, J. L., Van Molle, I., Roth, A. G., Tae, H. S., Gareiss, P. C., Jorgensen, W. L., Ciulli, A. & Crews, C. M. (2012). Angew. Chem. Int. Ed. 51, 11463–11467. PubMed PMC

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. PubMed PMC

Emsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. (2010). Acta Cryst. D66, 486–501. PubMed PMC

Fabregat, A., Sidiropoulos, K., Viteri, G., Forner, O., Marin-Garcia, P., Arnau, V., D’Eustachio, P., Stein, L. & Hermjakob, H. (2017). BMC Bioinformatics, 18, 142. PubMed PMC

Finn, R. D., Coggill, P., Eberhardt, R. Y., Eddy, S. R., Mistry, J., Mitchell, A. L., Potter, S. C., Punta, M., Qureshi, M., Sangrador-Vegas, A., Salazar, G. A., Tate, J. & Bateman, A. (2016). Nucleic Acids Res. 44, D279–D285. PubMed PMC

Gadd, M. S., Testa, A., Lucas, X., Chan, K.-H., Chen, W. Z., Lamont, D. J., Zengerle, M. & Ciulli, A. (2017). Nature Chem. Biol. 13, 514–521. PubMed PMC

Gore, S. et al. (2017). Structure, 25, 1916–1927. PubMed

Gore, S., Velankar, S. & Kleywegt, G. J. (2012). Acta Cryst. D68, 478–483. PubMed PMC

Groom, C. R., Bruno, I. J., Lightfoot, M. P. & Ward, S. C. (2016). Acta Cryst. B72, 171–179. PubMed PMC

Henderson, R. et al. (2012). Structure, 20, 205–214. PubMed PMC

Kinjo, A. R., Bekker, G. J., Suzuki, H., Tsuchiya, Y., Kawabata, T., Ikegawa, Y. & Nakamura, H. (2017). Nucleic Acids Res. 45, D282–D288. PubMed PMC

Kleywegt, G. J. (2000). Acta Cryst. D56, 249–265. PubMed

Kleywegt, G. J., Harris, M. R., Zou, J., Taylor, T. C., Wählby, A. & Jones, T. A. (2004). Acta Cryst. D60, 2240–2249. PubMed

Kleywegt, G. J. & Jones, T. A. (2002). Structure, 10, 465–472. PubMed

Koscielny, G. et al. (2017). Nucleic Acids Res. 45, D985–D994. PubMed PMC

Lawson, C. L. et al. (2011). Nucleic Acids Res. 39, D456–D464. PubMed PMC

Lee, W. C., Ohshiro, T., Matsubara, T., Izumi, Y. & Tanokura, M. (2006). J. Biol. Chem. 281, 32534–32539. PubMed

Lütteke, T. & von der Lieth, C. W. (2004). BMC Bioinformatics, 5, 69. PubMed PMC

Meldal, B. H. M. et al. (2015). Nucleic Acids Res. 43, D479–D484. PubMed PMC

Mir, S. et al. (2018). Nucleic Acids Res. 46, D486–D492. PubMed PMC

Montelione, G. T., Nilges, M., Bax, A., Güntert, P., Herrmann, T., Richardson, J. S., Schwieters, C. D., Vranken, W. F., Vuister, G. W., Wishart, D. S., Berman, H. M., Kleywegt, G. J. & Markley, J. L. (2013). Structure, 21, 1563–1570. PubMed PMC

Protein Data Bank (1971). Nature New Biol. 233, 223.

Read, R. J. et al. (2011). Structure, 19, 1395–1412. PubMed PMC

Richardson, J. S., Schneider, B., Murray, L. W., Kapral, G. J., Immormino, R. M., Headd, J. J., Richardson, D. C., Ham, D., Hershkovits, E., Williams, L. D., Keating, K. S., Pyle, A. M., Micallef, D., Westbrook, J. & Berman, H. M. (2008). RNA, 14, 465–481. PubMed PMC

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. PubMed

Sehnal, D., Svobodová Vařeková, R., Pravda, L., Ionescu, C. M., Geidl, S., Horský, V., Jaiswal, D., Wimmerová, M. & Koča, J. (2015). Nucleic Acids Res. 43, D369–D375. PubMed PMC

Shao, C. H., Yang, H. W., Westbrook, J. D., Young, J. Y., Zardecki, C. & Burley, S. K. (2017). Structure, 25, 458–468. PubMed PMC

Sillitoe, I., Lewis, T. E., Cuff, A., Das, S., Ashford, P., Dawson, N. L., Furnham, N., Laskowski, R. A., Lee, D., Lees, J. G., Lehtinen, S., Studer, R. A., Thornton, J. & Orengo, C. A. (2015). Nucleic Acids Res. 43, D376–D381. PubMed PMC

Smart, O. S., Horský, V., Gore, S., Svobodová Vařeková, R., Bendová, V., Kleywegt, G. J. & Velankar, S. (2018). Acta Cryst. D74, 228–236. PubMed PMC

Svobodova Varekova, R., Horsky, V., Sehnal, D., Bendova, V., Pravda, L. & Koca, J. (2017). Biophys. J. 112, 346a–347a.

Tagari, M., Newman, R., Chagoyen, M., Carazo, J. M. & Henrick, K. (2002). Trends Biochem. Sci. 27, 589. PubMed

The UniProt Consortium (2017). Nucleic Acids Res. 45, D158–D169. PubMed

Ulrich, E. L. et al. (2008). Nucleic Acids Res. 36, D402–D408. PubMed PMC

Vaezeslami, S., Mathes, E., Vasileiou, C., Borhan, B. & Geiger, J. H. (2006). J. Mol. Biol. 363, 687–701. PubMed

Velankar, S. et al. (2016). Nucleic Acids Res. 44, D385–D395. PubMed PMC

Westbrook, J. D., Shao, C. H., Feng, Z. K., Zhuravleva, M., Velankar, S. & Young, J. (2015). Bioinformatics, 31, 1274–1278. PubMed PMC

Yang, H., Peisach, E., Westbrook, J. D., Young, J., Berman, H. M. & Burley, S. K. (2016). J. Appl. Cryst. 49, 1081–1084. PubMed PMC

Young, J. Y. et al. (2017). Structure, 25, 536–545. PubMed PMC

Zwart, P. H., Grosse-Kunsteleve, R. W. & Adams, P. D. (2005). CCP4 Newsl. Protein Crystallogr. 42, contribution 10.