Thanks all, very interesting, so our methods are just needed to identify the crystallization impurities, when the trays have been thrown away ;-
Cheers, Jon.C. Sent from ProtonMail mobile -------- Original Message -------- On 3 Dec 2020, 22:31, Anastassis Perrakis wrote: > AlphaFold - or similar ideas that will surface up sooner or later - will > beyond doubt have major impact. The accuracy it demonstrated compared to > others is excellent. > > “Our” target (T1068) that was not solvable by MR with the homologous search > structure or a homology model (it was phased with Archimboldo, rather > easily), is easily solvable with the AlphaFold model as a search model. In > PHASER I get Rotation Z-score 17.9, translation Z-score 26.0, using defaults. > > imho what remains to be seen is: > > a. how and when will a prediction server be available? > b. even if training needs computing that will surely unaccessible to most, > will there be code that can be installed in a “reasonable” number of GPUs and > how fast will it be? > c. how do model quality metrics (that do not compared with the known answer) > correlate with the expected RMSD? AlphaFold, no matter how impressive, still > gets things wrong. > c. will the AI efforts now gear to ligand (fragment?) prediction with > similarly impressive performance? > > Exciting times. > > A. > >> On 3 Dec 2020, at 21:55, Jon Cooper >> <0000488a26d62010-dmarc-requ...@jiscmail.ac.uk> wrote: >> >> Hello. A quick look suggests that a lot of the test structures were solved >> by phaser or molrep, suggesting it is a very welcome improvement on homology >> modelling. It would be interesting to know how it performs with structures >> of new or uncertain fold, if there are any left these days. Without >> resorting to jokes about artificial intelligence, I couldn't make that out >> from the CASP14 website or the many excellent articles that have appeared. >> Best wishes, Jon Cooper. >> >> Sent from ProtonMail mobile >> >> -------- Original Message -------- >> On 3 Dec 2020, 11:17, Isabel Garcia-Saez < isabel.gar...@ibs.fr> 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/
