Deep-learning map segmentation for protein X-ray crystallographic structure determination

References

First citationAbadi, M., Agarwal, A., Barham, P., Brevdo, E., Chen, Z., Citro, C., Corrado, G. S., Davis, A., Dean, J., Devin, M., Ghemawat, S., Goodfellow, I., Harp, A., Irving, G., Isard, M., Jozefowicz, R., Jia, Y., Kaiser, L., Kudlur, M., Levenberg, J., Mané, D., Schuster, M., Monga, R., Moore, S., Murray, D., Olah, C., Shlens, J., Steiner, B., Sutskever, I., Talwar, K., Tucker, P., Vanhoucke, V., Vasudevan, V., Viégas, F., Vinyals, O., Warden, P., Wattenberg, M., Wicke, M., Yu, Y. & Zheng, X. (2015). TensorFlow. https://tensorflow.orgGoogle Scholar
First citationAbrahams, J. P. & Leslie, A. G. W. (1996). Acta Cryst. D52, 30–42.  CrossRef CAS Web of Science IUCr Journals 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 citationBaek, M., DiMaio, F., Anishchenko, I., Dauparas, J., Ovchinnikov, S., Lee, G. R., Wang, J., Cong, Q., Kinch, L. N., Schaeffer, R. D., Millán, C., Park, H., Adams, C., Glassman, C. R., DeGiovanni, A., Pereira, J. H., Rodrigues, A. V., van Dijk, A. A., Ebrecht, A. C., Opperman, D. J., Sagmeister, T., Buhlheller, C., Pavkov-Keller, T., Rathina­swamy, M. K., Dalwadi, U., Yip, C. K., Burke, J. E., Garcia, K. C., Grishin, N. V., Adams, P. D., Read, R. J. & Baker, D. (2021). Science, 373, 871–876.  Web of Science CrossRef CAS PubMed Google Scholar
First citationBerman, 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.  Web of Science CrossRef PubMed CAS Google Scholar
First citationBond, P. S. & Cowtan, K. D. (2022). Acta Cryst. D78, 1090–1098.  Web of Science CrossRef IUCr Journals Google Scholar
First citationBricogne, G. (1974). Acta Cryst. A30, 395–405.  CrossRef Web of Science IUCr Journals Google Scholar
First citationChen, J., Wu, L., Zhang, J., Zhang, L., Gong, D., Zhao, Y., Chen, Q., Huang, S., Yang, M., Yang, X., Hu, S., Wang, Y., Hu, X., Zheng, B., Zhang, K., Wu, H., Dong, Z., Xu, Y., Zhu, Y., Chen, X., Zhang, M., Yu, L., Cheng, F. & Yu, H. (2020). Sci. Rep. 10, 19196.  CrossRef PubMed Google Scholar
First citationChojnowski, G., Simpkin, A. J., Leonardo, D. A., Seifert-Davila, W., Vivas-Ruiz, D. E., Keegan, R. M. & Rigden, D. J. (2022). IUCrJ, 9, 86–97.  Web of Science CrossRef CAS PubMed IUCr Journals Google Scholar
First citationChollet, F. (2015). Keras: Deep Learning for Humans. https://keras.ioGoogle Scholar
First citationCowtan, K. (2008). Acta Cryst. D64, 83–89.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationCowtan, K. (2010). Acta Cryst. D66, 470–478.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationDall'Antonia, F. & Schneider, T. R. (2006). J. Appl. Cryst. 39, 618–619.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationElbasir, A., Mall, R., Kunji, K., Rawi, R., Islam, Z., Chuang, G. Y., Kolatkar, P. R. & Bensmail, H. (2020). Bioinformatics, 36, 1429–1438.  Web of Science CrossRef CAS PubMed Google Scholar
First citationElsliger, M.-A., Deacon, A. M., Godzik, A., Lesley, S. A., Wooley, J., Wüthrich, K. & Wilson, I. A. (2010). Acta Cryst. F66, 1137–1142.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationGodo, A., Aoki, K., Nakagawa, A. & Yagi, Y. (2022). IEEE Access. 10, 28760–28772.  Web of Science CrossRef Google Scholar
First citationHe, K., Zhang, X., Ren, S. & Sun, J. (2016). 2016 IEEE Conference on Computer Vision and Pattern Recognition (CVPR), pp. 770–778. Piscataway: IEEE.  Google Scholar
First citationJin, C., Gao, J., Shi, Z. & Zhang, H. (2021). Neurocomputing, 463, 265–274.  Web of Science CrossRef 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 citationKantardjieff, K. A. & Rupp, B. (2003). Protein Sci. 12, 1865–1871.  Web of Science CrossRef PubMed CAS Google Scholar
First citationKe, T.-W., Brewster, A. S., Yu, S. X., Ushizima, D., Yang, C. & Sauter, N. K. (2018). J. Synchrotron Rad. 25, 655–670.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationKhurana, S., Rawi, R., Kunji, K., Chuang, G. Y., Bensmail, H. & Mall, R. (2018). Bioinformatics, 34, 2605–2613.  Web of Science CrossRef CAS PubMed Google Scholar
First citationKingma, D. P. & Ba, J. (2014). arXiv:1412.6980.  Google Scholar
First citationKingston, R. L. & Millane, R. P. (2022). IUCrJ, 9, 648–665.  Web of Science CrossRef CAS PubMed IUCr Journals Google Scholar
First citationLeslie, A. G. W. (1987). Acta Cryst. A43, 134–136.  CrossRef CAS Web of Science IUCr Journals Google Scholar
First citationLunin, V. Y. (1988). Acta Cryst. A44, 144–150.  CrossRef CAS Web of Science IUCr Journals Google Scholar
First citationMatinyan, S., Filipcik, P. & Abrahams, J. P. (2024). Acta Cryst. A80, 1–17.  Web of Science CrossRef IUCr Journals Google Scholar
First citationMatthews, B. W. (1968). J. Mol. Biol. 33, 491–497.  CrossRef CAS PubMed Web of Science Google Scholar
First citationMiyaguchi, I., Sato, M., Kashima, A., Nakagawa, H., Kokabu, Y., Ma, B., Matsumoto, S., Tokuhisa, A., Ohta, M. & Ikeguchi, M. (2021). Sci. Rep. 11, 23599.  Web of Science CrossRef PubMed Google Scholar
First citationNicholls, R. A., Tykac, M., Kovalevskiy, O. & Murshudov, G. N. (2018). Acta Cryst. D74, 492–505.  Web of Science CrossRef IUCr Journals Google Scholar
First citationPan, T., Jin, S., Miller, M. D., Kyrillidis, A. & Phillips, G. N. (2023). IUCrJ, 10, 487–496.  Web of Science CrossRef CAS PubMed IUCr Journals Google Scholar
First citationPannu, N. S. & Skubák, P. (2023). Acta Cryst. D79, 339–344.  CrossRef IUCr Journals Google Scholar
First citationRonneberger, O., Fischer, P. & Brox, T. (2015). Medical Image Computing and Computer-Assisted Intervention – MICCAI 2015, edited by N. Navab, J. Hornegger, W. M. Wells & A. F. Frangi, pp. 234–241. Cham: Springer International Publishing.  Google Scholar
First citationSaood, A. & Hatem, I. (2021). BMC Med. Imaging, 21, 19.  Google Scholar
First citationSchneider, T. R. & Sheldrick, G. M. (2002). Acta Cryst. D58, 1772–1779.  Web of Science CrossRef CAS IUCr Journals Google Scholar
First citationSkubák, P. (2018). Acta Cryst. D74, 117–124.  Web of Science CrossRef IUCr Journals Google Scholar
First citationSkubák, P., Murshudov, G. N. & Pannu, N. S. (2004). Acta Cryst. D60, 2196–2201.  Web of Science CrossRef IUCr Journals Google Scholar
First citationSkubák, P. & Pannu, N. S. (2013). Nat. Commun. 4, 2777.  Web of Science PubMed Google Scholar
First citationSouza, A., Oliveira, L. B., Hollatz, S., Feldman, M., Olukotun, K., Holton, J. M., Cohen, A. E. & Nardi, L. (2019). arXiv:1904.11834.  Google Scholar
First citationUsón, I. & Sheldrick, G. M. (2018). Acta Cryst. D74, 106–116.  Web of Science CrossRef IUCr Journals Google Scholar
First citationVingelmann, P. & Fitzek, F. H. (2020). NVIDIA CUDA. https://developer.nvidia.com/cuda-toolkitGoogle Scholar
First citationWang, B.-C. (1985). Methods Enzymol. 115, 90–112.  CrossRef CAS PubMed Google Scholar
First citationWang, P. H., Zhu, Y. H., Yang, X. & Yu, D. J. (2023). Anal. Biochem. 663, 115020.  Web of Science CrossRef PubMed Google Scholar
First citationWeichenberger, C. X. & Rupp, B. (2014). Acta Cryst. D70, 1579–1588.  Web of Science CrossRef IUCr Journals Google Scholar
First citationWojdyr, M. (2022). J. Open Source Softw. 7, 4200.  CrossRef Google Scholar
First citationYann, M. & Tang, Y. (2016). Proc. AAAI Conf. Artif. Intell. 30, https://doi.org/10.1609/aaai.v30i1.10150Google Scholar
First citationZhang, K. Y. J. & Main, P. (1990). Acta Cryst. A46, 41–46.  CrossRef CAS IUCr Journals Google Scholar

留言 (0)

沒有登入
gif