Thanks Andrea for this!
One more for crystallization:
Ng JT., Dekker C., Kroemer M., Osborne M., von Delft F., (2014), Acta D,
70, 2702 - 2718
On 03/08/2021 12:43, Thorn, Dr. Andrea 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 <http://www.thorn-lab.de> | www.insidecorona.net
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