Bernhard What qualifies? Good question. There are plenty of books on AI/machine learning but, as always, it is more efficient/lazier to read reviews than the books themselves. I think the London Review of Books allows limited access to its articles so most should be able to read this https://www.lrb.co.uk/the-paper/v43/n02/paul-taylor/insanely-complicated-hopelessly-inadequate?referrer=https%3A%2F%2Fwww.google.com%2F It might be interesting (though perhaps not useful) to classify the examples for macromolecular structure determination in to categories such as GOFAI etc. However, this particular term is rather pejorative as it would mean describing the developers as old fashioned!
Colin -----Original Message----- From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Bernhard Rupp Sent: 03 August 2021 21:00 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] AI papers in experimental macromolecular structure determination Maybe we should get to the root of this - what qualifies as machine learning and what not? Do nonparametric predictors such as KDE qualify? https://www.ruppweb.org/mattprob/default.html Happy toa dd to the confusion. -----Original Message----- From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Tim Gruene Sent: Tuesday, August 3, 2021 11:59 To: CCP4BB@JISCMAIL.AC.UK Subject: Re: [ccp4bb] AI papers in experimental macromolecular structure determination Hello Andrea, profile fitting, like it is done in mosflm (https://doi.org/10.1107/S090744499900846X) or evalccd, or ... probably also qualify as AI/machine learning. Best wishes, Tim On Tue, 3 Aug 2021 11:43:06 +0000 "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<http://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 > > 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/ -- -- Tim Gruene Head of the Centre for X-ray Structure Analysis Faculty of Chemistry University of Vienna Phone: +43-1-4277-70202 GPG Key ID = A46BEE1A ######################################################################## 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/ ######################################################################## 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/ -- This e-mail and any attachments may contain confidential, copyright and or privileged material, and are for the use of the intended addressee only. 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