The success rate of processed predicted models in molecular replacement: implications for experimental phasing in the AlphaFold era

References

First citationAbramson, J., Adler, J., Dunger, J., Evans, R., Green, T., Pritzel, A., Ronneberger, O., Willmore, L., Ballard, A. J., Bambrick, J., Bodenstein, S. W., Evans, D. A., Hung, C., O'Neill, M., Reiman, D., Tunyasuvunakool, K., Wu, Z., Žemgulytė, A., Arvaniti, E., Beattie, C., Bertolli, O., Bridgland, A., Cherepanov, A., Congreve, M., Cowen-Rivers, A. I., Cowie, A., Figurnov, M., Fuchs, F. B., Gladman, H., Jain, R., Khan, Y. A., Low, C. M. R., Perlin, K., Potapenko, A., Savy, P., Singh, S., Stecula, A., Thillaisundaram, A., Tong, C., Yakneen, S., Zhong, E. D., Zielinski, M., Žídek, A., Bapst, V., Kohli, P., Jaderberg, M., Hassabis, D. & Jumper, J. M. (2024). Nature, 630, 493–500.  Web of Science CrossRef CAS PubMed Google Scholar
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 citationBarbarin-Bocahu, I. & Graille, M. (2022). Acta Cryst. D78, 517–531.  Web of Science CrossRef IUCr Journals Google Scholar
First citationBerman, H., Henrick, K. & Nakamura, H. (2003). Nat. Struct. Mol. Biol. 10, 980.  Web of Science CrossRef Google Scholar
First citationBibby, J., Keegan, R. M., Mayans, O., Winn, M. D. & Rigden, D. J. (2012). Acta Cryst. D68, 1622–1631.  Web of Science CrossRef IUCr Journals Google Scholar
First citationBond, P. S. & Cowtan, K. D. (2022). Acta Cryst. D78, 1090–1098.  Web of Science CrossRef IUCr Journals Google Scholar
First citationBreugel, M. van, Rosa e Silva, I. & Andreeva, A. (2022). Commun. Biol. 5, 312.  Google Scholar
First citationCaballero, I., Sammito, M., Millán, C., Lebedev, A., Soler, N. & Usón, I. (2018). Acta Cryst. D74, 194–204.  Web of Science CrossRef IUCr Journals Google Scholar
First citationChowdhury, R., Bouatta, N., Biswas, S., Floristean, C., Kharkar, A., Roy, K., Rochereau, C., Ahdritz, G., Zhang, J., Church, G. M., Sorger, P. K. & AlQuraishi, M. (2022). Nat. Biotechnol. 40, 1617–1623.  Web of Science CrossRef CAS PubMed Google Scholar
First citationCretin, G., Galochkina, T., Vander Meersche, Y., de Brevern, A. G., Postic, G. & Gelly, J. C. (2022). Nucleic Acids Res. 50, W732–W738.  Web of Science CrossRef CAS PubMed Google Scholar
First citationEl Omari, K., Duman, R., Mykhaylyk, V., Orr, C. M., Latimer-Smith, M., Winter, G., Grama, V., Qu, F., Bountra, K., Kwong, H. S., Romano, M., Reis, R. I., Vogeley, L., Vecchia, L., Owen, C. D., Wittmann, S., Renner, M., Senda, M., Matsugaki, N., Kawano, Y., Bowden, T. A., Moraes, I., Grimes, J. M., Mancini, E. J., Walsh, M. A., Guzzo, C. R., Owens, R. J., Jones, E. Y., Brown, D. G., Stuart, D. I., Beis, K. & Wagner, A. (2023). Commun. Chem. 6, 219.  Web of Science CrossRef PubMed Google Scholar
First citationEvans, R., O'Neill, M., Pritzel, P., Antropova, N., Senior, A., Green, T., Žídek, A., Bates, R., Blackwell, S., Yim, J., Ronneberger, O., Bodenstein, S., Zielinski, M., Bridgland, A., Potapenko, A., Cowie, A., Tunyasuvunakool, K., Jain, R., Clancy, E. Kohli, P., Jumper, J. & Hassabis, D. (2021). bioRxiv, 2021.10.04.463034.  Google Scholar
First citationFu, R., Su, W. & He, H. (2022). Crystals, 12, 1674.  Web of Science CrossRef Google Scholar
First citationJing, X., Wu, F., Luo, X. & Xu, J. (2024). Proc. Natl Acad. Sci. USA, 121, e2308788121.  Web of Science CrossRef PubMed Google Scholar
First citationJohnson, L. S., Eddy, S. R. & Portugaly, E. (2010). BMC Bioinformatics, 11, 431.  Google Scholar
First citationJumper, J., Evans, R., Pritzel, A., Green, T., Figurnov, M., Ronneberger, O., Tunyasuvunakool, K., Bates, R., Žídek, A., Potapenko, A., Bridgland, A., Meyer, C., Kohl, S. A. A., Ballard, A. J., Cowie, A., Romera-Paredes, B., Nikolov, S., Jain, R., Adler, J., Back, T., Petersen, S., Reiman, D., Clancy, E., Zielinski, M., Steinegger, M., Pacholska, M., Berghammer, T., Bodenstein, S., Silver, D., Vinyals, O., Senior, A. W., Kavukcuoglu, K., Kohli, P. & Hassabis, D. (2021). Nature, 596, 583–589.  Web of Science CrossRef CAS PubMed Google Scholar
First citationKandathil, S. M., Lau, A. M. & Jones, D. T. (2024). bioRxiv, 2024.03.25.586696.  Google Scholar
First citationKarlin, D. G. (2024). J. Gen. Virol. 105, https://doi.org/10.1099/jgv.0.001948Web of Science CrossRef Google Scholar
First citationKrissinel, E. (2012). J. Mol. Biochem. 1, 76–85.  CAS PubMed Google Scholar
First citationKrissinel, E., Lebedev, A. A., Uski, V., Ballard, C. B., Keegan, R. M., Kovalevskiy, O., Nicholls, R. A., Pannu, N. S., Skubák, P., Berrisford, J., Fando, M., Lohkamp, B., Wojdyr, M., Simpkin, A. J., Thomas, J. M. H., Oliver, C., Vonrhein, C., Chojnowski, G., Basle, A., Purkiss, A., Isupov, M. N., McNicholas, S., Lowe, E., Triviño, J., Cowtan, K., Agirre, J., Rigden, D. J., Uson, I., Lamzin, V., Tews, I., Bricogne, G., Leslie, A. G. W. & Brown, D. G. (2022). Acta Cryst. D78, 1079–1089.  Web of Science CrossRef IUCr Journals Google Scholar
First citationKshirsagar, M., Meller, A., Humphreys, I., Sledzieski, S., Xu, Y., Dodhia, R., Horvitz, E., Berger, B., Bowman, G., Lavista Ferres, J., Baker, D. & Baek, M. (2024). Research Square, https://doi.org/10.21203/rs.3.rs-4215086/v1Google Scholar
First citationKumar, P. & Woolfson, D. N. (2021). Bioinformatics, 37, 4575–4577.  Web of Science CrossRef CAS PubMed Google Scholar
First citationLi, Z., Liu, X., Chen, W., Shen, F., Bi, H., Ke, G. & Zhang, L. (2022). bioRxiv, 2022.08.04.502811.  Google Scholar
First citationLiebschner, D., Afonine, P. V., Baker, M. L., Bunkóczi, G., Chen, V. B., Croll, T. I., Hintze, B., Hung, L.-W., Jain, S., McCoy, A. J., Moriarty, N. W., Oeffner, R. D., Poon, B. K., Prisant, M. G., Read, R. J., Richardson, J. S., Richardson, D. C., Sammito, M. D., Sobolev, O. V., Stockwell, D. H., Terwilliger, T. C., Urzhumtsev, A. G., Videau, L. L., Williams, C. J. & Adams, P. D. (2019). Acta Cryst. D75, 861–877.  Web of Science CrossRef IUCr Journals Google Scholar
First citationLin, Z., Akin, H., Rao, R., Hie, B., Zhu, Z., Lu, W., Smetanin, N., Verkuil, R., Kabeli, O., Shmueli, Y., dos Santos Costa, A., Fazel-Zarandi, M., Sercu, T., Candido, S. & Rives, A. (2023). Science, 379, 1123–1130.  Web of Science CrossRef CAS PubMed Google Scholar
First citationMadaj, R., Martinez-Goikoetxea, M., Kaminski, K., Ludwiczak, J. & Dunin-Horkawicz, S. (2024). bioRxiv, 2024.03.07.583852.  Google Scholar
First citationMadeo, G., Savojardo, C., Manfredi, M., Martelli, P. L. & Casadio, R. (2023). Bioinformatics, 39, btad495.  Web of Science CrossRef PubMed Google Scholar
First citationMcCoy, A. J., Sammito, M. D. & Read, R. J. (2022). Acta Cryst. D78, 1–13.  Web of Science CrossRef IUCr Journals Google Scholar
First citationMcCoy, A. J., Grosse-Kunstleve, R. W., Adams, P. D., Winn, M. D., Storoni, L. C. & Read, R. J. (2007). J. Appl. Cryst. 40, 658–674.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationMcNicholas, S., Potterton, E., Wilson, K. S. & Noble, M. E. M. (2011). Acta Cryst. D67, 386–394.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationMillán, C., Keegan, R. M., Pereira, J., Sammito, M. D., Simpkin, A. J., McCoy, A. J., Lupas, A. N., Hartmann, M. D., Rigden, D. J. & Read, R. J. (2021). Proteins, 89, 1752–1769.  Web of Science PubMed Google Scholar
First citationMirdita, M., Schütze, K., Moriwaki, Y., Heo, L., Ovchinnikov, S. & Steinegger, M. (2022). Nat. Methods, 19, 679–682.  Web of Science CrossRef CAS PubMed Google Scholar
First citationMirdita, M., von den Driesch, L., Galiez, C., Martin, M. J., Söding, J. & Steinegger, M. (2017). Nucleic Acids Res. 45, D170–D176.  Web of Science CrossRef CAS PubMed Google Scholar
First citationOeffner, R. D., Afonine, P. V., Millán, C., Sammito, M., Usón, I., Read, R. J. & McCoy, A. J. (2018). Acta Cryst. D74, 245–255.  Web of Science CrossRef IUCr Journals Google Scholar
First citationOeffner, R. D., Croll, T. I., Millán, C., Poon, B. K., Schlicksup, C. J., Read, R. J. & Terwilliger, T. C. (2022). Acta Cryst. D78, 1303–1314.  Web of Science CrossRef IUCr Journals Google Scholar
First citationPereira, J., Simpkin, A. J., Hartmann, M. D., Rigden, D. J., Keegan, R. M. & Lupas, A. N. (2021). Proteins, 89, 1687–1699.  Web of Science CrossRef CAS PubMed Google Scholar
First citationPoon, B. K., Terwilliger, T. C. & Adams, P. D. (2024). Protein Sci. 33, e4992.  Web of Science CrossRef PubMed Google Scholar
First citationQian, B., Raman, S., Das, R., Bradley, P., McCoy, A. J., Read, R. J. & Baker, D. (2007). Nature, 450, 259–264.  Web of Science CrossRef PubMed CAS Google Scholar
First citationRead, R. J. & McCoy, A. J. (2016). Acta Cryst. D72, 375–387.  Web of Science CrossRef IUCr Journals Google Scholar
First citationRemmert, M., Biegert, A., Hauser, A. & Söding, J. (2012). Nat. Methods, 9, 173–175.  Web of Science CrossRef CAS Google Scholar
First citationRichardson, L., Allen, B., Baldi, G., Beracochea, M., Bileschi, M. L., Burdett, T., Burgin, J., Caballero-Pérez, J., Cochrane, G., Colwell, L. J., Curtis, T., Escobar-Zepeda, A., Gurbich, T. A., Kale, V., Korobeynikov, A., Raj, S., Rogers, A. B., Sakharova, E., Sanchez, S., Wilkinson, D. J. & Finn, R. D. (2023). Nucleic Acids Res. 51, D753–D759.   Web of Science CrossRef CAS PubMed Google Scholar
First citationRigden, D. J., Thomas, J. M. H., Simkovic, F., Simpkin, A., Winn, M. D., Mayans, O. & Keegan, R. M. (2018). Acta Cryst. D74, 183–193.  Web of Science CrossRef IUCr Journals Google Scholar
First citationRodríguez, D. D., Grosse, C., Himmel, S., González, C., de Ilarduya, I. M., Becker, S., Sheldrick, G. M. & Usón, I. (2009). Nat. Methods, 6, 651–653.  Web of Science PubMed Google Scholar
First citationRuiz-Serra, V., Pontes, C., Milanetti, E., Kryshtafovych, A., Lepore, R. & Valencia, A. (2021). Proteins, 89, 1888–1900.  Web of Science CAS PubMed Google Scholar
First citationSammito, M., Meindl, K., de Ilarduya, I. M., Millán, C., Artola-Recolons, C., Hermoso, J. A. & Usón, I. (2014). FEBS J. 281, 4029–4045.  Web of Science CrossRef CAS PubMed Google Scholar
First citationSammito, M., Millán, C., Rodríguez, D. D., de Ilarduya, I. M., Meindl, K., De Marino, I., Petrillo, G., Buey, R. M., de Pereda, J. M., Zeth, K., Sheldrick, G. M. & Usón, I. (2013). Nat. Methods, 10, 1099–1101.  Web of Science CrossRef CAS PubMed Google Scholar
First citationSánchez Rodríguez, F., Simpkin, A. J., Davies, O. R., Keegan, R. M. & Rigden, D. J. (2020). Acta Cryst. D76, 962–970.  Web of Science CrossRef IUCr Journals Google Scholar
First citationSimkovic, F., Thomas, J. M. H., Keegan, R. M., Winn, M. D., Mayans, O. & Rigden, D. J. (2016). IUCrJ, 3, 259–270.  Web of Science CrossRef CAS PubMed IUCr Journals Google Scholar
First citationSimpkin, A. J., Caballero, I., McNicholas, S., Stevenson, K., Jiménez, E., Sánchez Rodríguez, F., Fando, M., Uski, V., Ballard, C., Chojnowski, G., Lebedev, A., Krissinel, E., Usón, I., Rigden, D. J. & Keegan, R. M. (2023). Acta Cryst. D79, 806–819.  Web of Science CrossRef IUCr Journals Google Scholar
First citationSimpkin, A. J., Elliott, L. G., Stevenson, K., Krissinel, E., Rigden, D. & Keegan, R. M. (2022). bioRxiv, 2022.06.30.497974.  Google Scholar
First citationSimpkin, A. J., Mesdaghi, S., Sánchez Rodríguez, F., Elliott, L., Murphy, D. L., Kryshtafovych, A., Keegan, R. M. & Rigden, D. J. (2023). Proteins, 91, 1616–1635.  Web of Science CrossRef CAS PubMed Google Scholar
First citationSimpkin, A. J., Thomas, J. M. H., Simkovic, F., Keegan, R. M. & Rigden, D. J. (2019). Acta Cryst. D75, 1051–1062.  Web of Science CrossRef IUCr Journals Google Scholar
First citationSteinegger, M., Meier, M., Mirdita, M., Vöhringer, H., Haunsberger, S. J. & Söding, J. (2019). BMC Bioinformatics, 20, 473.  Google Scholar
First citationSteinegger, M. & Söding, J. (2017). Nat. Biotechnol. 35, 1026–1028.  Web of Science CrossRef CAS PubMed Google Scholar
First citationSuzek, B. E., Wang, Y., Huang, H., McGarvey, P. B., Wu, C. H. & UniProt Consortium (2015). Bioinformatics, 31, 926–932.  Web of Science CrossRef PubMed

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