I don't have a list to add here, as my review on the topic awaits feedback on the corrections (self-advertisement π) but perhaps we should consider that machine learning and AI are two different beasts. Admittingly, I don't always make a proper distinction either.
Surely, many of us get their heads around machine learning, which usually covers so called shallow learners that firmly sit in well-known concepts of statistics. This type of machine learning doesn't require many resources and is accessible to almost anyone with an average laptop. Plenty of software in MX and EM use these tools and no-one every thinks about them. I think, Andrea, perhaps, was looking more into the direction of AI (based on so many cryo-EM references listed π, where this is a standard tool), which requires a lot more understanding and thought as well as resources and would appear to many as a magic black box. This type of machine learning has only recently taken off due to huge leaps in hardware development, which many of us can't afford to buy, unless it is provided through some shared resource. Having said that, an average graphics card GPU is often a good start. And if one isn't the book reading kind (usually due to lack of time), there are lots of good blogs, videos and other online resources to get one into the basics. The papers that should clearly be added, are those for protein structure prediction, as, in a way, they determine a structure, albeit with a different kind of experiment: https://science.sciencemag.org/content/early/2021/07/19/science.abj8754 https://www.nature.com/articles/s41586-021-03819-2 Cheers M ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Nave, Colin (DLSLtd,RAL,LSCI) <000064fdcfc6624b-dmarc-requ...@jiscmail.ac.uk> Sent: 04 August 2021 09:34 To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] AI papers in experimental macromolecular structure determination 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, 1705β1716. > - Morris, R. J. (2004). Acta Cryst D. 60, 2133β2143. > > 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, 854β865. > - Al-Azzawi, A., Ouadou, A., Tanner, J. J. & Cheng, J. (2019). BMC > Bioinformatics. 20, 1β26. > - George, B., Assaiya, A., Roy, R. J., Kembhavi, A., Chauhan, R., > Paul, G., Kumar, J. & Philip, N. S. (2021). Commun Biol. 4, 1β12. > - Lata, K. R., Penczek, P. & Frank, J. (1995). Ultramicroscopy. 58, > 381β391. > - Nguyen, N. P., Ersoy, I., Gotberg, J., Bunyak, F. & White, T. A. > (2021). BMC Bioinformatics. 22, 1β28. > - Wang, F., Gong, H., Liu, G., Li, M., Yan, C., Xia, T., Li, X. & > Zeng, J. (2016). Journal of Structural Biology. 195, 325β336. > - Wong, H. C., Chen, J., Mouche, F., Rouiller, I. & Bern, M. (2004). > Journal of Structural Biology. 145, 157β167. > > Motion description in Cryo-EM: > - Matsumoto, S., Ishida, S., Araki, M., Kato, T., Terayama, K. & > Okuno, Y. (2021). Nat Mach Intell. 3, 153β160. > - Zhong, E. D., Bepler, T., Berger, B. & Davis, J. H. (2021). Nat > Methods. 18, 176β185. > > Local resolution: > - Avramov, T. K., Vyenielo, D., Gomez-Blanco, J., Adinarayanan, S., > Vargas, J. & Si, D. (2019). Molecules. 24, 1181. > - RamΓrez-Aportela, E., Mota, J., Conesa, P., Carazo, J. M. & Sorzano, > C. O. S. (2019). IUCrJ. 6, 1054β1063. > - (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, 911β917. > - Li, R., Si, D., Zeng, T., Ji, S. & He, J. (2016). 2016 IEEE > International Conference on Bioinformatics and Biomedicine (BIBM), > Vol. pp. 41β46. > - Si, D., Ji, S., Nasr, K. A. & He, J. (2012). Biopolymers. 97, > 698β708. > - 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, 1β22. > - 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, 753β763. > > Crystallization: > - Liu, R., Freund, Y. & Spraggon, G. (2008). Acta Cryst D. 64, > 1187β1195. > - (2004). Methods. 34, 390β407. > - 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, > 1361β1366. > - 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, 2216β2225. > > 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, 655β670. > > 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., BaslΓ©, A., Murshudov, G. > N., Waterman, D. G. & Evans, G. (2020). IUCrJ. 7, 342β354. > > Ligand recognition: > Kowiel, M., Brzezinski, D., Porebski, P. J., Shabalin, I. G., > Jaskolski, M. & Minor, W. (2019). Bioinformatics. 35, 452β461. > > 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, UniversitΓ€t > 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<http://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<http://www.jiscmail.ac.uk/CCP4BB>, a > mailing list hosted by www.jiscmail.ac.uk<http://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<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by www.jiscmail.ac.uk<http://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<http://www.jiscmail.ac.uk/CCP4BB>, a mailing list hosted by www.jiscmail.ac.uk<http://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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