Improving macromolecular structure refinement with metal-coordination restraints

References

First citationAgirre, J., Atanasova, M., Bagdonas, H., Ballard, C. B., Baslé, A., Beilsten-Edmands, J., Borges, R. J., Brown, D. G., Burgos-Mármol, J. J., Berrisford, J. M., Bond, P. S., Caballero, I., Catapano, L., Chojnowski, G., Cook, A. G., Cowtan, K. D., Croll, T. I., Debreczeni, J. É., Devenish, N. E., Dodson, E. J., Drevon, T. R., Emsley, P., Evans, G., Evans, P. R., Fando, M., Foadi, J., Fuentes-Montero, L., Garman, E. F., Gerstel, M., Gildea, R. J., Hatti, K., Hekkelman, M. L., Heuser, P., Hoh, S. W., Hough, M. A., Jenkins, H. T., Jiménez, E., Joosten, R. P., Keegan, R. M., Keep, N., Krissinel, E. B., Kolenko, P., Kovalevskiy, O., Lamzin, V. S., Lawson, D. M., Lebedev, A. A., Leslie, A. G. W., Lohkamp, B., Long, F., Malý, M., McCoy, A. J., McNicholas, S. J., Medina, A., Millán, C., Murray, J. W., Murshudov, G. N., Nicholls, R. A., Noble, M. E. M., Oeffner, R., Pannu, N. S., Parkhurst, J. M., Pearce, N., Pereira, J., Perrakis, A., Powell, H. R., Read, R. J., Rigden, D. J., Rochira, W., Sammito, M., Sánchez Rodríguez, F., Sheldrick, G. M., Shelley, K. L., Simkovic, F., Simpkin, A. J., Skubak, P., Sobolev, E., Steiner, R. A., Stevenson, K., Tews, I., Thomas, J. M. H., Thorn, A., Valls, J. T., Uski, V., Usón, I., Vagin, A., Velankar, S., Vollmar, M., Walden, H., Waterman, D., Wilson, K. S., Winn, M. D., Winter, G., Wojdyr, M. & Yamashita, K. (2023). Acta Cryst. D79, 449–461.  Web of Science CrossRef IUCr Journals Google Scholar
First citationAragão, D., Mitchell, E. P., Frazão, C. F., Carrondo, M. A. & Lindley, P. F. (2008). Acta Cryst. D64, 665–674.  CrossRef IUCr Journals Google Scholar
First citationBazayeva, M., Andreini, C. & Rosato, A. (2024). Acta Cryst. D80, 362–376.  CrossRef IUCr Journals Google Scholar
First citationBishop, C. M. (2006). Pattern Recognition and Machine Learning. Berlin, Heidelberg: Springer-Verlag.  Google Scholar
First citationBolton, R., Machelett, M. M., Stubbs, J., Axford, D., Caramello, N., Catapano, L., Malý, M., Rodrigues, M. J., Cordery, C., Tizzard, G. J., MacMillan, F., Engilberge, S., von Stetten, D., Tosha, T., Sugimoto, H., Worrall, J. A. R., Webb, J. S., Zubkov, M., Coles, S., Mathieu, E., Steiner, R. A., Murshudov, G., Schrader, T. E., Orville, A. M., Royant, A., Evans, G., Hough, M. A., Owen, R. L. & Tews, I. (2024). Proc. Natl Acad. Sci. USA, 121, e2308478121.  CrossRef PubMed Google Scholar
First citationCarugo, O. & Djinović Carugo, K. (2005). Trends Biochem. Sci. 30, 213–219.  Web of Science CrossRef PubMed CAS Google Scholar
First citationCordero, B., Gómez, V., Platero-Prats, A. E., Revés, M., Echeverría, J., Cremades, E., Barragán, F. & Alvarez, S. (2008). Dalton Trans., pp. 2832–2838.  Google Scholar
First citationCrosilla, F., Beinat, A., Fusiello, A., Maset, E. & Visintini, D. (2019). Advanced Procrustes Analysis Models in Photogrammetric Computer Vision. Cham: Springer International.  Google Scholar
First citationDimitropoulos, D., Ionides, J. & Henrick, K. (2006). Curr. Protoc. Bioinformatics, 15, 14.  CrossRef Google Scholar
First citationDryden, I. L. & Mardia, K. V. (2016). Statistical Shape Analysis, with Applications in R, 2nd ed. Chichester: John Wiley & Sons.  Google Scholar
First citationEmsley, P., Lohkamp, B., Scott, W. G. & Cowtan, K. (2010). Acta Cryst. D66, 486–501.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationGisriel, C. J., Zhou, K., Huang, H.-L., Debus, R. J., Xiong, Y. & Brudvig, G. W. (2020). Joule, 4, 2131–2148.  CrossRef CAS Google Scholar
First citationGražulis, S., Chateigner, D., Downs, R. T., Yokochi, A. F. T., Quirós, M., Lutterotti, L., Manakova, E., Butkus, J., Moeck, P. & Le Bail, A. (2009). J. Appl. Cryst. 42, 726–729.  Web of Science CrossRef IUCr Journals Google Scholar
First citationGreenwood, N. & Earnshaw, A. (1997). Chemistry of the Elements, 2nd ed. Oxford: Butterworth-Heinemann.  Google Scholar
First citationHarding, M. M., Nowicki, M. W. & Walkinshaw, M. D. (2010). Crystallogr. Rev. 16, 247–302.  Web of Science CrossRef CAS Google Scholar
First citationHattne, J., Shi, D., Glynn, C., Zee, C.-T., Gallagher-Jones, M., Martynowycz, M. W., Rodriguez, J. A. & Gonen, T. (2018). Structure, 26, 759–766.  Web of Science CrossRef CAS PubMed Google Scholar
First citationHemsworth, G. R., González-Pacanowska, D. & Wilson, K. S. (2013). Biochem. J. 456, 81–88.  CrossRef CAS PubMed Google Scholar
First citationKoval', T., Švecová, L., Østergaard, L. H., Skalova, T., Dušková, J., Hašek, J., Kolenko, P., Fejfarová, K., Stránský, J., Trundová, M. & Dohnálek, J. (2019). Sci. Rep. 9, 13700.  Web of Science PubMed Google Scholar
First citationLandrum, G. (2016). Rdkit. https://github.com/rdkit/rdkit/releases/tag/Release_2016_09_4.  Google Scholar
First citationLewandowski, E. M., Skiba, J., Torelli, N. J., Rajnisz, A., Solecka, J., Kowalski, K. & Chen, Y. (2015). Chem. Commun. 51, 6186–6189.  CrossRef CAS Google Scholar
First citationLong, F., Nicholls, R. A., Emsley, P., Gražulis, S., Merkys, A., Vaitkus, A. & Murshudov, G. N. (2017). Acta Cryst. D73, 112–122.  Web of Science CrossRef IUCr Journals Google Scholar
First citationMalý, M., Diederichs, K., Dohnálek, J. & Kolenko, P. (2020). IUCrJ, 7, 681–692.  Web of Science CrossRef PubMed IUCr Journals Google Scholar
First citationMatsumoto, Y., Tosha, T., Pisliakov, A. V., Hino, T., Sugimoto, H., Nagano, S., Sugita, Y. & Shiro, Y. (2012). Nat. Struct. Mol. Biol. 19, 238–245.  Web of Science CrossRef CAS PubMed Google Scholar
First citationMoriarty, N. W., Grosse-Kunstleve, R. W. & Adams, P. D. (2009). Acta Cryst. D65, 1074–1080.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationMoser, J., Lange, C., Krausze, J., Rebelein, J., Schubert, W.-D., Ribbe, M. W., Heinz, D. W. & Jahn, D. (2013). Proc. Natl Acad. Sci. USA, 110, 2094–2098.  CrossRef CAS PubMed Google Scholar
First citationPutignano, V., Rosato, A., Banci, L. & Andreini, C. (2018). Nucleic Acids Res. 46, D459–D464.  Web of Science CrossRef CAS PubMed Google Scholar
First citationSilverman, B. W. (1981). J. R. Stat. Soc. Ser. B Stat. Methodol. 43, 97–99.   CrossRef Google Scholar
First citationSmart, O. S., Sharff, A., Holstein, J., Womack, T., Flensburg, C., Keller, P., Paciorek, W., Vonrhein, C. & Bricogne, G. (2021). Grade2, version 1.6.0. Global Phasing Ltd, Cambridge, United Kingdom.  Google Scholar
First citationTouw, W. G., van Beusekom, B., Evers, J. M. G., Vriend, G. & Joosten, R. P. (2016). Acta Cryst. D72, 1110–1118.  Web of Science CrossRef IUCr Journals Google Scholar
First citationVagin, A. A., Steiner, R. A., Lebedev, A. A., Potterton, L., Mc­Nicholas, S., Long, F. & Murshudov, G. N. (2004). Acta Cryst. D60, 2184–2195.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationWojdyr, M. (2022). J. Open Source Softw. 7, 4200.  CrossRef Google Scholar
First citationYamashita, K., Palmer, C. M., Burnley, T. & Murshudov, G. N. (2021). Acta Cryst. D77, 1282–1291.  Web of Science CrossRef IUCr Journals Google Scholar
First citationYano, J., Kern, J., Irrgang, K.-D., Latimer, M. J., Bergmann, U., Glatzel, P., Pushkar, Y., Biesiadka, J., Loll, B., Sauer, K., Messinger, J., Zouni, A. & Yachandra, V. K. (2005). Proc. Natl Acad. Sci. 102, 12047–12052.  Web of Science CrossRef PubMed CAS Google Scholar
First citationZheng, H., Chordia, M. D., Cooper, D. R., Chruszcz, M., Müller, P., Sheldrick, G. M. & Minor, W. (2014). Nat. Protoc. 9, 156–170.  Web of Science CrossRef CAS PubMed Google Scholar

View original article
ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY

留言 (0)

沒有登入
gif
format_indent_decrease