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Design of Cyclic Peptides Targeting Protein-Protein Interactions using AlphaFold
We developed a cyclic peptide complex offset to enable the structural prediction of target proteins and cyclic peptide complexes and found AlphaFold2 with a cyclic peptide complex offset can predict structures with high accuracy. We also applied the cyclic peptide complex offset to the binder hallucination protocol of AfDesign, a de novo protein design method using AlphaFold, and we could design a high predicted local-distance difference test and lower separated binding energy per unit interface area than the native MDM2/p53 structure. Furthermore, the method was applied to 12 other protein-peptide complexes and one protein-protein complex. Our approach shows that it is possible to design putative cyclic peptide sequences targeting PPI.
Takatsugu Kosugi, Masahito Ohue
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Solubility-aware protein binding peptide design using AlphaFold
New protein{\textendash}protein interactions (PPIs) are being identified, but PPIs have different physicochemical properties compared …
Takatsugu Kosugi, Masahito Ohue
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Quantitative Estimate of Protein-Protein Interaction Targeting Drug-likeness
Author’s final version of the manuscript accepted for the IEEE CIBCB 2021 conference. © 2021 IEEE.
Takatsugu Kosugi, Masahito Ohue
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