One more: BraggNet: integrating Bragg peaks using neural networks B. Sullivan, R. Archibald, J. Azadmanesh, V. G. Vandavasi, P. S. Langan, L. Coates, V. Lynch and P. Langan J. Appl. Cryst. (2019). 52, 854-863
Pavel On Tue, Aug 3, 2021 at 4:53 AM Thorn, Dr. Andrea < andrea.th...@uni-hamburg.de> wrote: > Dear colleagues, > > I have compiled a list of papers that cover the application of AI/machine > learning methods in single-crystal structure determination (mostly > macromolecular crystallography) and single-particle Cryo-EM. The draft list > is attached below. > > > > If I missed any papers, please let me know. I will send the final list > back here, for the benefit of all who are interested in the topic. > > > > Best wishes, > > > > > > Andrea. > > > > > > __ > > General: > > - Gopalakrishnan, V., Livingston, G., Hennessy, D., Buchanan, B. & > Rosenberg, J. M. (2004). Acta Cryst D. 60, 1705–1716. > > - Morris, R. J. (2004). Acta Cryst D. 60, 2133–2143. > > > > Micrograph preparation: > > - (2020). Journal of Structural Biology. 210, 107498. > > > > Particle Picking: > > - Sanchez-Garcia, R., Segura, J., Maluenda, D., Carazo, J. M. & Sorzano, > C. O. S. (2018). IUCrJ. 5, 854–865. > > - Al-Azzawi, A., Ouadou, A., Tanner, J. J. & Cheng, J. (2019). BMC > Bioinformatics. 20, 1–26. > > - George, B., Assaiya, A., Roy, R. J., Kembhavi, A., Chauhan, R., Paul, > G., Kumar, J. & Philip, N. S. (2021). Commun Biol. 4, 1–12. > > - Lata, K. R., Penczek, P. & Frank, J. (1995). Ultramicroscopy. 58, > 381–391. > > - Nguyen, N. P., Ersoy, I., Gotberg, J., Bunyak, F. & White, T. A. (2021). > BMC Bioinformatics. 22, 1–28. > > - Wang, F., Gong, H., Liu, G., Li, M., Yan, C., Xia, T., Li, X. & Zeng, J. > (2016). Journal of Structural Biology. 195, 325–336. > > - Wong, H. C., Chen, J., Mouche, F., Rouiller, I. & Bern, M. (2004). > Journal of Structural Biology. 145, 157–167. > > > > Motion description in Cryo-EM: > > - Matsumoto, S., Ishida, S., Araki, M., Kato, T., Terayama, K. & Okuno, Y. > (2021). Nat Mach Intell. 3, 153–160. > > - Zhong, E. D., Bepler, T., Berger, B. & Davis, J. H. (2021). Nat Methods. > 18, 176–185. > > > > Local resolution: > > - Avramov, T. K., Vyenielo, D., Gomez-Blanco, J., Adinarayanan, S., > Vargas, J. & Si, D. (2019). Molecules. 24, 1181. > > - Ramírez-Aportela, E., Mota, J., Conesa, P., Carazo, J. M. & Sorzano, C. > O. S. (2019). IUCrJ. 6, 1054–1063. > > - (2021). QAEmap: A Novel Local Quality Assessment Method for Protein > Crystal Structures Using Machine Learning. > > > > Map post-processing: > > - Sanchez-Garcia, R., Gomez-Blanco, J., Cuervo, A., Carazo, J. M., > Sorzano, C. O. S. & Vargas, J. (2020). BioRxiv. 2020.06.12.148296. > > > > Secondary structure assignment in map: > > - Subramaniya, S. R. M. V., Terashi, G. & Kihara, D. (2019). Nat Methods. > 16, 911–917. > > - Li, R., Si, D., Zeng, T., Ji, S. & He, J. (2016). 2016 IEEE > International Conference on Bioinformatics and Biomedicine (BIBM), Vol. pp. > 41–46. > > - Si, D., Ji, S., Nasr, K. A. & He, J. (2012). Biopolymers. 97, 698–708. > > - He, J. & Huang, S.-Y. Brief Bioinform. > > - Lyu, Z., Wang, Z., Luo, F., Shuai, J. & Huang, Y. (2021). Frontiers in > Bioengineering and Biotechnology. 9,. > > - Mostosi, P., Schindelin, H., Kollmannsberger, P. & Thorn, A. (2020). > Angewandte Chemie International Edition. > > > > Automatic structure building: > > - Alnabati, E. & Kihara, D. (2020). Molecules. 25, 82. > > - Si, D., Moritz, S. A., Pfab, J., Hou, J., Cao, R., Wang, L., Wu, T. & > Cheng, J. (2020). Sci Rep. 10, 1–22. > > - Moritz, S. A., Pfab, J., Wu, T., Hou, J., Cheng, J., Cao, R., Wang, L. & > Si, D. (2019). > > - Chojnowski, G., Pereira, J. & Lamzin, V. S. (2019). Acta Cryst D. 75, > 753–763. > > > > Crystallization: > > - Liu, R., Freund, Y. & Spraggon, G. (2008). Acta Cryst D. 64, 1187–1195. > > - (2004). Methods. 34, 390–407. > > - Bruno, A. E., Charbonneau, P., Newman, J., Snell, E. H., So, D. R., > Vanhoucke, V., Watkins, C. J., Williams, S. & Wilson, J. (2018). PLOS ONE. > 13, e0198883. > > > > Crystal centering: > > - Ito, S., Ueno, G. & Yamamoto, M. (2019). J Synchrotron Rad. 26, > 1361–1366. > > - Crystal centering using deep learning in X-ray crystallography. > > - Elbasir, A., Moovarkumudalvan, B., Kunji, K., Kolatkar, P. R., Mall, R. > & Bensmail, H. (2019). Bioinformatics. 35, 2216–2225. > > > > Diffraction image analysis: > > - Czyzewski, A., Krawiec, F., Brzezinski, D., Porebski, P. J. & Minor, W. > (2021). Expert Systems with Applications. 174, 114740. > > > > Peak search in serial crystallography: > > Ke, T.-W., Brewster, A. S., Yu, S. X., Ushizima, D., Yang, C. & Sauter, N. > K. (2018). J Synchrotron Rad. 25, 655–670. > > > > Space group assignment from diffraction image (small molecules): > > Aguiar, J. A., Gong, M. L., Unocic, R. R., Tasdizen, T. & Miller, B. D. > (2019). Science Advances. 5, eaaw1949. > > > > Data quality assessment in MX: > > - Vollmar, M., Parkhurst, J. M., Jaques, D., Baslé, A., Murshudov, G. N., > Waterman, D. G. & Evans, G. (2020). IUCrJ. 7, 342–354. > > > > Ligand recognition: > > Kowiel, M., Brzezinski, D., Porebski, P. J., Shabalin, I. G., Jaskolski, > M. & Minor, W. (2019). Bioinformatics. 35, 452–461. > > > > Prediction of missing atoms in small molecular structures: > > Thomas, N., Smidt, T., Kearnes, S., Yang, L., Li, L., Kohlhoff, K. & > Riley, P. (2018). > > > > ADP estimation (small molecules): > > Gagner, V. A., Jensen, M. & Katona, G. (2021). Mach. Learn.: Sci. Technol. > 2, 035033. > > > > > > -- > > Dr. Andrea Thorn | group leader > > andrea.th...@uni-hamburg.de > > > > Institute for Nanostructure and Solid State Physics, Universität Hamburg > > Luruper Chaussee 149 / Bldg. 610 (HARBOR) | 22761 Hamburg | Germany > > Tel. +49 (0)40 42838 3651 > > www.thorn-lab.de | www.insidecorona.net > > > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > ######################################################################## To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 This message was issued to members of www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by www.jiscmail.ac.uk, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/
