I can't see prediction of cyclic peptide example
kimdn opened this issue · 6 comments
2023_Cyclic peptide structure prediction and design using AlphaFold
mentions
"Example scripts for structure prediction, sequence design, and hallucination are available at https://github.com/sokrypton/ColabDesign/blob/main/af/examples/af_cyc_design.ipynb"
However, I can't see prediction of cyclic peptide example at https://github.com/sokrypton/ColabDesign/blob/main/af/examples/af_cyc_design.ipynb
I see fixbb and hallucination examples only.
Hi! The same happend to me, do you find the code where is the prediction of cyclic peptides?
Thank you
See this notebook (look at the instructions at the bottom):
https://colab.research.google.com/github/sokrypton/ColabDesign/blob/gamma/af/examples/predict.ipynb
See this notebook (look at the instructions at the bottom): https://colab.research.google.com/github/sokrypton/ColabDesign/blob/gamma/af/examples/predict.ipynb
@sokrypton
Thanks. I could run this notebook file with my sequence (APCPPTVLRF) --> (I enclosed my peptide sequence with () since it is thought to be cyclic peptide.
All predicted pdb files (e.g., best.pdb, model_1_ptm_seed0.pdb etc) are near cyclic but not perfectly closed cyclic as
@kimdn I think this is just a pymol drawing issue, but they should be close enough to form bond.
@kimdn I think this is just a pymol drawing issue, but they should be close enough to form bond.
@sokrypton Got it. Above picture was obtained by chimeraX.
With pymol (and showing 'main chain'), indeed I got perfectly closed form of cyclic peptide as
as I see AfCycDesign paper
Of course, if I didn't show 'main chain', still I see unclosed form as
However, I wouldn't worry as you commented.
Thank you very much for the fast response @sokrypton