Yes - our CASP15 target H1157 contained intramolecular and
inter-molecular SS bonds - the former were well predicted but the latter
were not:
https://predictioncenter.org/casp15/multimer_results.cgi?target=H1157
The article discussing this aspect (as well a few other CASP15 targets)
is at the proofs stage in Proteins.
Ciao
Pietro
On 13-07-2023 18:07, Guillaume Gaullier wrote:
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> 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> wrote:
Does anybody know if cis-peptides are predicted by the AI tools
(AlphaFold2, ColabFold, or ESM-2)?
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