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<http://www.thorn-lab.de> | www.insidecorona.net


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