Reconciling Cooperativity Definition in PROTACs and Molecular Glues: Thermodynamic Dissection into PPI and Ligand Entropic Contributions
This paper resolves the controversy surrounding Cooperativity definitions in PROTACs and molecular glues by demonstrating that the apparent negative Cooperativity observed in "partial-embedded" models is actually an entropic penalty from restricting the exposed mass of large ligands, thereby revealing that true positive Protein-Protein Interaction (PPI) Cooperativity exists once this ligand entropy cost is subtracted.