This repository is based on the AfDesign binder hallucination protocol from ColabDesign, published by Dr. Sergey Ovchinnikov on GitHub.
Cyclic peptide complex offset was applied to AfDesign to enable hallucination of cyclic peptide binders to target proteins.
Cyclic Peptide Binder Hallucination with Google Colab
Cyclic Peptide Binder Hallucination with Jupyter Notebook
cyclic_peptide_binder_design.ipynb
cyc_peptide_binder_ptm_1YCR_A_13_0081_pssm_semigreedy.mp4
Cyclic peptide complex offset is an offset for structure prediction and hallucination of protein-cyclic peptide complex.
Example of relative position encoding of a hypothetical 20-residue protein and a 10-residue peptide. Default complex offset on the left and cyclic peptide complex offset on the right.
Kosugi, T.; Ohue, M. Design of Cyclic Peptides Targeting Protein–Protein Interactions Using AlphaFold Int. J. Mol. Sci. 2023, 24, 13257. doi:10.3390/ijms241713257
Kosugi, T.; Ohue, M. Design of Cyclic Peptides Targeting Protein-Protein Interactions Using AlphaFold bioRxiv 2023, doi:10.1101/2023.08.20.554056.