Hi Andrea, Here is something interesting on the extraction of information on protein dynamics from cryo-EM data:
https://doi.org/10.1038/s42256-020-00290-y Best, Tushar. On Tue, 3 Aug 2021 at 19:48, Shekhar Mande <[email protected]> wrote: > 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 < > [email protected]> 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 <[email protected]> >> 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 >> [email protected] >> >> 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 >> >> >> >> >> >> >> >> >> >> >> När du har kontakt med oss på Uppsala universitet med e-post så innebär >> det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör >> det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ >> >> E-mailing Uppsala University means that we will process your personal >> data. For more information on how this is performed, please read here: >> http://www.uu.se/en/about-uu/data-protection-policy >> >> ------------------------------ >> >> To unsubscribe from the CCP4BB list, click the following link: >> https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 >> > > > -- > शेखर चिं मांडे > महानिदेशक, वैज्ञानिक तथा औद्योगिक अनुसंधान परिषद् तथा > सचिव, वैज्ञानिक तथा औद्योगिक अनुसंधान विभाग > अनुसंधान भवन, २ रफ़ी मार्ग, नई दिल्ली ११०००१ > Shekhar C. Mande > Director General, Council of Scientific and Industrial Research and > Secretary, Department of Scientific and Industrial Research, Govt of India > New Delhi > > ------------------------------ > > To unsubscribe from the CCP4BB list, click the following link: > https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 > -- Tushar B. Raskar Postdoctoral fellow, Fraser lab, University of California San Francisco, 600 16th street, Genntech Hall Room S476, San Francisco, CA 94143 Former address: 1033, Pearson Lab, Hamburg Advanced Research Centre for Bioorganic Chemistry (HARBOR), Notkestrasse 85, 22607 Hamburg. ######################################################################## 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/
