btw, if anyone has any leverage to the people making the CASP#14 pages, having info in acronyms (e.g. GDT) accessible by a simple “mouse over” instead of re-directing to the explanation page would be handy.
In any case, the Casp web-pages in general, leave quite a bit to be desired for the average user - they seem more like an "API for humans” and less concerned about modern design principles, to put it mildly. Tassos On Dec 4, 2020, at 8:53, Joana Pereira <joana.pere...@tuebingen.mpg.de<mailto:joana.pere...@tuebingen.mpg.de>> wrote: Hi everybody, As one of the persons playing with the CASP14 data before all news came out, I can answer some of the questions raised in this thread. - "Does anyone know how AlphaFold performs on sequences with little conservation?" One of the things we looked at was how the accuracy of the models was dependent on the Neff (number of effective sequences, relates to how deep alignments are for that sequence and, thus, to the number of homologs and the conservation of the sequence). What we could see is that, basically, in CASP14 it does not anymore and that (near-)singleton sequences could be modeled with a pretty good accuracy. - "It would be interesting to know how it performs with structures of new or uncertain fold." It does pretty well! Similarly to the Neff relationship, we also see a basically flat line at a GDT of 70-80 at any level of target difficulty. Of course the accuracy is slightly higher for easy targets (those for which there are templates in the PDB), but to have a GDT of around 70 in Free-Modelling, hard targets, is quite impressive. - "I don't think they have all the side chain placement so perfect as to be able to predict the fold and how a compound or another protein binds" Yap, sidechains remain the poorest modeled parts. Still, those modeled by AlphaFold were the closest to the "reality" of the target... - "I'm curious how well AlphaFold would do on an Intrinsically Disordered Protein (IDP)" Oh yes, that is a super good point and I have been thinking about it too. Maybe one should start throwing some IDPs into CASP too :) There's the CAID experiment but, on its current state, AlphaFold would not be possible to test. Best wishes Joana --- Dr. Joana Pereira Postdoctoral Researcher Department of Protein Evolution Max Planck Institute for Developmental Biology Max-Planck-Ring 5 72076 Tübingen GERMANY On 03.12.20 23:46, Reza Khayat wrote: Does anyone know how AlphaFold performs on sequences with little conservation? Virus and phage proteins are like this. Their structures are homologous, but sequence identity can be less than 10%. Reza Reza Khayat, PhD Associate Professor City College of New York Department of Chemistry and Biochemistry New York, NY 10031 ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK><mailto:CCP4BB@JISCMAIL.AC.UK> on behalf of Anastassis Perrakis <a.perra...@nki.nl><mailto:a.perra...@nki.nl> Sent: Thursday, December 3, 2020 5:31 PM To: CCP4BB@JISCMAIL.AC.UK<mailto:CCP4BB@JISCMAIL.AC.UK> Subject: [EXTERNAL] Re: [ccp4bb] AlphaFold: more thinking and less pipetting (?) 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<mailto: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<mailto: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<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.nature.com_articles_d41586-2D020-2D03348-2D4&d=DwMGaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=5lc5MUokcPdJZuiKvx3xkaHGMFTkSQHuwMu3HoQZUNA&s=FjJEUNt1oYyfCSZk105Z-QvYSPRKxaj1NGZOmqJsXKw&e=> 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/<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.ibs.fr_&d=DwMGaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=5lc5MUokcPdJZuiKvx3xkaHGMFTkSQHuwMu3HoQZUNA&s=YlBw2nUGdJg2OpSa9WKUs8bJxcGcNDihK6rZy-M-d0Q&e=> ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMGaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=5lc5MUokcPdJZuiKvx3xkaHGMFTkSQHuwMu3HoQZUNA&s=x-2GXzG8eqhqC4BAqzPekybM7m-MvbZCTkuEasQNook&e=> ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMGaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=5lc5MUokcPdJZuiKvx3xkaHGMFTkSQHuwMu3HoQZUNA&s=x-2GXzG8eqhqC4BAqzPekybM7m-MvbZCTkuEasQNook&e=> ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1<https://urldefense.proofpoint.com/v2/url?u=https-3A__www.jiscmail.ac.uk_cgi-2Dbin_WA-2DJISC.exe-3FSUBED1-3DCCP4BB-26A-3D1&d=DwMGaQ&c=4NmamNZG3KTnUCoC6InoLJ6KV1tbVKrkZXHRwtIMGmo&r=1DzJFW0v6TgEhkW1gy_-ke-RbtvS1fzEbD5_hcb9Up0&m=5lc5MUokcPdJZuiKvx3xkaHGMFTkSQHuwMu3HoQZUNA&s=x-2GXzG8eqhqC4BAqzPekybM7m-MvbZCTkuEasQNook&e=> ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 -- Postdoctoral Researcher Department of Protein Evolution Max Planck Institute for Developmental Biology Max-Planck-Ring 5 72076 Tübingen GERMANY ________________________________ 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/
