colbyford / pemfauxlizumab

Pembrolizumab-like Antibody Hallucination using AlphaFold2

Pemfauxlizumab: Pembrolizumab-like Antibody Hallucination using AlphaFold2

Companion Repository for: Am I Hallucinating or Can AI Now Design Cancer-Curing Antibodies?

Colby T. Ford, Ph.D.

Comparison of the binding angles of Pembrolizumab (in green) and Pemfauxlizumab (in blue) bound to PD-1 (in purple).

Process

Structure Hallucinations

• Run hallucinate.ipynb notebook.

Structure Prep for Docking

• Run the steps in data_prep.md.

Resources

• AlphaFold2-based hallucinations were performed with ColabDesign, created by Sergey Ovchinnikov
• HADDOCK 2.4 docking system in Docker: https://github.com/colbyford/HADDOCKer/tree/main/HADDOCK2.4
• Protein images were made using: https://3dproteinimaging.com/protein-imager/