This is very much anecdotal - in my experience, AF2 tends to put the Cys residues in the disulfide bridge adjacent to each other, sometimes with roughly the correct side chain orientation.
It doesn't build/refine the S-S bond, becuase I don't think it knows how to. Best, Dave Dr David C. Briggs CSci MRSB Principal Laboratory Research Scientist Signalling and Structural Biology Lab The Francis Crick Institute London, UK == about.me/david_briggs<http://about.me/david_briggs> ________________________________ From: CCP4 bulletin board <CCP4BB@JISCMAIL.AC.UK> on behalf of Guillaume Gaullier <guillaume.gaull...@kemi.uu.se> Sent: Thursday, July 13, 2023 5:07:57 PM To: CCP4BB@JISCMAIL.AC.UK <CCP4BB@JISCMAIL.AC.UK> Subject: Re: [ccp4bb] AI and cis-peptides External Sender: Use caution. Interesting. Has someone similarly looked at whether AlphaFold predicts disulfide bridges? Guillaume On 13 Jul 2023, at 15:12, Randy John Read <rj...@cam.ac.uk<mailto:rj...@cam.ac.uk>> wrote: I’m not sure about other methods, but AlphaFold does predict peptides in both cis and trans configurations. In a recent paper, Osnat Herzberg and John Moult show that it was pretty successful in predicting proline cis-peptides, among the novel structures in the CASP15 set of targets (https://www.pnas.org/doi/10.1073/pnas.2221745120). For non-proline cis-peptides, I’m not aware of published work but Tristan Croll has shown me examples of correctly-predicted non-proline cis-peptides, including cases where some of the related structures in the PDB have an incorrect trans configuration. This implies that AlphaFold is not slavishly reproducing what it has seen during training. Best wishes, Randy Read On 13 Jul 2023, at 13:56, Oliviero Carugo <oliviero.car...@univie.ac.at<mailto:oliviero.car...@univie.ac.at>> wrote: Does anybody know if cis-peptides are predicted by the AI tools (AlphaFold2, ColabFold, or ESM-2)? ######################################################################## 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 http://www.jiscmail.ac.uk/CCP4BB, a mailing list hosted by http://www.jiscmail.ac.uk/, terms & conditions are available at https://www.jiscmail.ac.uk/policyandsecurity/ ----- Randy J. Read Department of Haematology, University of Cambridge Cambridge Institute for Medical Research Tel: +44 1223 336500 The Keith Peters Building Hills Road E-mail: rj...@cam.ac.uk<mailto:rj...@cam.ac.uk> Cambridge CB2 0XY, U.K. www-structmed.cimr.cam.ac.uk<http://www-structmed.cimr.cam.ac.uk/> ######################################################################## 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/ VARNING: Klicka inte på länkar och öppna inte bilagor om du inte känner igen avsändaren och vet att innehållet är säkert. CAUTION: Do not click on links or open attachments unless you recognise the sender and know the content is safe. När du har kontakt med oss på Uppsala universitet med e-post så innebär det att vi behandlar dina personuppgifter. För att läsa mer om hur vi gör det kan du läsa här: http://www.uu.se/om-uu/dataskydd-personuppgifter/ E-mailing Uppsala University means that we will process your personal data. For more information on how this is performed, please read here: http://www.uu.se/en/about-uu/data-protection-policy ________________________________ To unsubscribe from the CCP4BB list, click the following link: https://www.jiscmail.ac.uk/cgi-bin/WA-JISC.exe?SUBED1=CCP4BB&A=1 The Francis Crick Institute Limited is a registered charity in England and Wales no. 1140062 and a company registered in England and Wales no. 06885462, with its registered office at 1 Midland Road London NW1 1AT ######################################################################## 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/
