Hi Jon, I use AF3 quite often to look at domain boundaries by sequence but not necessarily by their spatial arrangement. This is because protein-protein interactions at least in all cases I’ve tried were not predicted correctly. I have number of Fab-Antigen complexes solved using x-ray crystallography but have not deposited in the PDB for various reasons. Using those molecules as an input to predict interaction interfaces were all plain wrong. Up until last week I did not have even one case where I’d call AF3 wrong for predicting a fold of a protein (a globular one)because all predictions were not only correct but also agree with topological features published within UniProt. Please, take a look at FATP2 (https://www.uniprot.org/uniprotkb/O14975/entry#structure) and you probably will agree that it is wrongly predicted structure. It is predicted with high confidence (dark blue) which is even more surprising. So my message in short would be: trust to some degree but don’t get surprised if it is wrong for cases without analogues in the PDB.
Vaheh From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> On Behalf Of Jon Cooper Sent: Saturday, October 5, 2024 9:48 AM To: CCP4BB@JISCMAIL.AC.UK Subject: [ccp4bb] AlphaFold3 Just wondering if anyone has any comments on, or concrete experiences with, alphafold3. I might try to cobble something together for Crystallography News (he says, having missed the main Nature paper, ahem). My googling has only given me hype and gripe so far ;-0 ;-0 Best wishes, Jon Cooper. jon.b.coo...@protonmail.com<mailto:jon.b.coo...@protonmail.com> Sent from Proton Mail Android ######################################################################## 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://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/<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/
