I'm curious how well AlphaFold would do on an Intrinsically Disordered Protein (IDP), would it recognize that it is an "IDP" or predict that it has a structure (or structures)? It would be interesting to test such a sequence and see what comes out. Possibly AlphaFold might be the best IDP predictor too.
Joel On 4 Dec 2020, at 6:29, Jon Cooper <0000488a26d62010-dmarc-requ...@jiscmail.ac.uk<mailto:0000488a26d62010-dmarc-requ...@jiscmail.ac.uk>> wrote: Hello James, that's really strange - I've used refmac et al., to do poor man's energy minimizations of models and they've generally come out fine, unless the restraints, etc, are wildly off-target. I wasn't playing with X-ray weights though, since there never was a dataset, of course. Cheers, Jon.C. Sent from ProtonMail mobile -------- Original Message -------- On 4 Dec 2020, 01:34, James Holton < jmhol...@lbl.gov<mailto:jmhol...@lbl.gov>> wrote: It is a major leap forward for structure prediction for sure. A hearty congratulations to all those teams over all those years. The part I don't understand is the accuracy. If we understand what holds molecules together so well, then why is it that when I refine an X-ray structure and turn the X-ray weight term down to zero ... the molecule blows up in my face? -James Holton MAD Scientist On 12/3/2020 3:17 AM, Isabel Garcia-Saez wrote: Dear all, Just commenting that after the stunning performance of AlphaFold that uses AI from Google maybe some of us we could dedicate ourselves to the noble art of gardening, baking, doing Chinese Calligraphy, enjoying the clouds pass or everything together (just in case I have already prepared my subscription to Netflix). https://www.nature.com/articles/d41586-020-03348-4 Well, I suppose that we still have the structures of complexes (at the moment). I am wondering how the labs will have access to this technology in the future (would it be for free coming from the company DeepMind - Google?). It seems that they have already published some code. Well, exciting times. Cheers, Isabel Isabel Garcia-Saez PhD Institut de Biologie Structurale Viral Infection and Cancer Group (VIC)-Cell Division Team 71, Avenue des Martyrs CS 10090 38044 Grenoble Cedex 9 France Tel.: 00 33 (0) 457 42 86 15 e-mail: isabel.gar...@ibs.fr<mailto:isabel.gar...@ibs.fr> FAX: 00 33 (0) 476 50 18 90 http://www.ibs.fr/ ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 ######################################################################## 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/
