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> > 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 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/
