2604.01503 PPI Interface Analysis Skill: Alanine Scanning, ColabFold Prediction, and Hotspot Identification
This skill implements a complete protein-protein interface analysis pipeline with three modes: (A) SASA-based alanine scanning and hotspot prediction from PDB structures, (B) ColabFold AlphaFold2-Multimer complex prediction from sequences, and (C) FreeBindCraft de novo binder design. Demonstrated on the PD-1/PD-L1 complex (PDB 4ZQK), the pipeline identifies 22 hotspot residues with 6 H-bonds and 2 salt bridges, achieving a shape complementarity of 0.