Abramson, 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
Agirre, 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
Barbarin-Bocahu, I. & Graille, M. (2022). Acta Cryst. D78, 517–531. Web of Science CrossRef IUCr Journals Google Scholar
Berman, H., Henrick, K. & Nakamura, H. (2003). Nat. Struct. Mol. Biol. 10, 980. Web of Science CrossRef Google Scholar
Bibby, 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
Bond, P. S. & Cowtan, K. D. (2022). Acta Cryst. D78, 1090–1098. Web of Science CrossRef IUCr Journals Google Scholar
Breugel, M. van, Rosa e Silva, I. & Andreeva, A. (2022). Commun. Biol. 5, 312. Google Scholar
Caballero, 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
Chowdhury, 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
Cretin, 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
El 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
Evans, 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
Fu, R., Su, W. & He, H. (2022). Crystals, 12, 1674. Web of Science CrossRef Google Scholar
Jing, X., Wu, F., Luo, X. & Xu, J. (2024). Proc. Natl Acad. Sci. USA, 121, e2308788121. Web of Science CrossRef PubMed Google Scholar
Johnson, L. S., Eddy, S. R. & Portugaly, E. (2010). BMC Bioinformatics, 11, 431. Google Scholar
Jumper, 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
Kandathil, S. M., Lau, A. M. & Jones, D. T. (2024). bioRxiv, 2024.03.25.586696. Google Scholar
Karlin, D. G. (2024). J. Gen. Virol. 105, https://doi.org/10.1099/jgv.0.001948. Web of Science CrossRef Google Scholar
Krissinel, E. (2012). J. Mol. Biochem. 1, 76–85. CAS PubMed Google Scholar
Krissinel, 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
Kshirsagar, 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/v1. Google Scholar
Kumar, P. & Woolfson, D. N. (2021). Bioinformatics, 37, 4575–4577. Web of Science CrossRef CAS PubMed Google Scholar
Li, Z., Liu, X., Chen, W., Shen, F., Bi, H., Ke, G. & Zhang, L. (2022). bioRxiv, 2022.08.04.502811. Google Scholar
Liebschner, 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
Lin, 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
Madaj, R., Martinez-Goikoetxea, M., Kaminski, K., Ludwiczak, J. & Dunin-Horkawicz, S. (2024). bioRxiv, 2024.03.07.583852. Google Scholar
Madeo, G., Savojardo, C., Manfredi, M., Martelli, P. L. & Casadio, R. (2023). Bioinformatics, 39, btad495. Web of Science CrossRef PubMed Google Scholar
McCoy, A. J., Sammito, M. D. & Read, R. J. (2022). Acta Cryst. D78, 1–13. Web of Science CrossRef IUCr Journals Google Scholar
McCoy, 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
McNicholas, 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
Millán, 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
Mirdita, 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
Mirdita, 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
Oeffner, 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
Oeffner, 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
Pereira, 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
Poon, B. K., Terwilliger, T. C. & Adams, P. D. (2024). Protein Sci. 33, e4992. Web of Science CrossRef PubMed Google Scholar
Qian, 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
Read, R. J. & McCoy, A. J. (2016). Acta Cryst. D72, 375–387. Web of Science CrossRef IUCr Journals Google Scholar
Remmert, M., Biegert, A., Hauser, A. & Söding, J. (2012). Nat. Methods, 9, 173–175. Web of Science CrossRef CAS Google Scholar
Richardson, 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
Rigden, 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
Rodríguez, 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
Ruiz-Serra, V., Pontes, C., Milanetti, E., Kryshtafovych, A., Lepore, R. & Valencia, A. (2021). Proteins, 89, 1888–1900. Web of Science CAS PubMed Google Scholar
Sammito, 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
Sammito, 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
Sánchez 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
Simkovic, 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
Simpkin, 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
Simpkin, A. J., Elliott, L. G., Stevenson, K., Krissinel, E., Rigden, D. & Keegan, R. M. (2022). bioRxiv, 2022.06.30.497974. Google Scholar
Simpkin, 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
Simpkin, 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
Steinegger, M., Meier, M., Mirdita, M., Vöhringer, H., Haunsberger, S. J. & Söding, J. (2019). BMC Bioinformatics, 20, 473. Google Scholar
Steinegger, M. & Söding, J. (2017). Nat. Biotechnol. 35, 1026–1028. Web of Science CrossRef CAS PubMed Google Scholar
Suzek, B. E., Wang, Y., Huang, H., McGarvey, P. B., Wu, C. H. & UniProt Consortium (2015). Bioinformatics, 31, 926–932. Web of Science CrossRef PubMed
留言 (0)