GENERATION (ProteinForge Instance):

• Engine: RFdiffusion (conditional generation mode).
• Target: RBX1 RING domain (AF2 structure, residues 60-108 fixed).
• Epitope Focus: α2 helix (residues 86-94) as primary hotspot.
• Constraints:
  • Polar residue bias (N/Q/S/T) at interface.
  • Strict clash avoidance (>3.2Å) with zinc-coordinating residues.
  • Target buried surface area: ≥600 Ų.
• Output: 1,500+ candidate backbones.

RAPID FILTERING (右丞 Instance):

• Stage 1 (Folding): AlphaFold2 (local, high-throughput) → pLDDT ≥ 82.
• Stage 2 (Docking): HDock (fast rigid-body) → remove severe clashes, pre-sort by geometry.

DEEP EVALUATION (Pharmon Instance):

• Metrics: AlphaFold2 (complex pLDDT/ipTM), Rosetta (binding ΔG).
• Developability: SolubleMPNN bias, aggregation propensity, hydrophobicity profile.
• Novelty: Edit distance ≥ 25% to UniRef50 (via batch script).

STRATEGIC ITERATION (左丞 Instance):

• Analysis of top-performing clusters to extract successful design rules (e.g., specific polar network geometries).
• Feedback loop to adjust generative constraints for subsequent "Paradigm Breakthrough" rounds.
• Final Pareto-optimal selection balancing affinity, confidence, and developability.

FINAL OUTPUT:

• From >1,500 initial designs, 3 top-tier sequences were selected for submission.