> On Jul 13, 2023, at 8:12 AM, Randy John Read <rj...@cam.ac.uk> wrote: > > > External Email Warning: Do not click links or open attachments unless you > recognize the sender and expect the content. UTMB Email Phishing > Awareness<https://www.utmb.edu/infosec/resources/phishawareness> > > 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). >
Indeed, back in late 2020, at the CASP14 conference, Osnat showed that the AF-predicted model of her protein containing a cis-proline fit the X-ray map way better than the model that she built de novo with a trans-proline. Considering that these days many (most?) of us are working with 3A+ resolution cryoEM maps in which the conformation of the main chain is uncertain (main chain oxygen bumps are invisible), the question of trans/cis-prolines is omnipresent. Sometimes (most often?) it can be answered with the help of an AF model. > 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. Thank you for this note. This is another confirmation that these days we need to carefully examine all discrepancies between our de-novo built structures and AF models. Petr Leiman > > Best wishes, > > Randy Read > >> On 13 Jul 2023, at 13:56, Oliviero Carugo <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 > Cambridge CB2 0XY, U.K. > 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 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/ ######################################################################## 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/
