In particle picking, you may wish to include the following:

George, B., Assaiya, A., Roy, R.J. *et al.* CASSPER is a semantic
segmentation-based particle picking algorithm for single-particle
cryo-electron microscopy. *Commun Biol* 4, 200 (2021).
https://doi.org/10.1038/s42003-021-01721-1

On Tue, Aug 3, 2021 at 9:17 PM Guillaume Gaullier <
guillaume.gaull...@icm.uu.se> wrote:

> Hello,
>
> In the particle picking section, you may want to include these two:
>
> Wagner T, Merino F, Stabrin M, Moriya T, Antoni C, Apelbaum A, Hagel P,
> Sitsel O, Raisch T, Prumbaum D, et al (2019) SPHIRE-crYOLO is a fast and
> accurate fully automated particle picker for cryo-EM. Communications
> Biology 2: 218 https://doi.org/10.1038/s42003-019-0437-z
>
> Bepler T, Morin A, Rapp M, Brasch J, Shapiro L, Noble AJ & Berger B (2019)
> Positive-unlabeled convolutional neural networks for particle picking in
> cryo-electron micrographs. Nat Methods: 1–8
> https://doi.org/10.1038/s41592-019-0575-8
>
> And this paper on micrograph denoising could go in the "micrograph
> preparation" section I suppose, or in its own section:
>
> Bepler T, Kelley K, Noble AJ & Berger B (2020) Topaz-Denoise: general deep
> denoising models for cryoEM and cryoET. Nature Communications 11: 5208
> https://doi.org/10.1038/s41467-020-18952-1
>
> I hope this is useful.
> Cheers,
>
> Guillaume
>
>
> On 3 Aug 2021, at 13:43, 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
>
>
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शेखर चिं मांडे
महानिदेशक, वैज्ञानिक तथा औद्योगिक अनुसंधान परिषद् तथा
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अनुसंधान भवन, २ रफ़ी मार्ग, नई दिल्ली ११०००१
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Director General, Council of Scientific and Industrial Research and
Secretary, Department of Scientific and Industrial Research, Govt of India
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