Andrea, you may want to include this one:
Using support vector machines to improve elemental ion identification in macromolecular crystal structures. Morshed N, Echols N, Adams PD Acta Cryst. D71, 1147-58 (2015). 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/
