Geometric Relevance Is Not Sufficient: Evaluating Focused Post-Training Supervision in Diffusion Docking

Michael Brown, Maryam Rahimimovassagh, Mehdi Yazdani-Jahromi, Sanjeda Sara Jennifer, Ivan Garibay

Diffusion-based molecular docking requires learning a corrective score field across a broad corruption distribution, yet individual pose errors can differ substantially in their structural consequences. This creates a post-training conflict between preserving broad score-field coverage and concentrating supervision on corrections that appear more relevant to docking geometry. Using DiffDock, a fixed-budget study compares broad continuation with torsional supervision focused on Cartesian consequence or conditional target consistency, and with a broad/focused mixture. Evaluation separates fixed score fidelity, generated-pose quality, best-of-10 sampling capacity, and confidence-selected Top-1 docking performance. At <5 Angstrom, broad continuation had the highest mean Top-1 success among trained policies, and focused or mixed supervision showed no consistent advantage under the tested budget. The starting model had better fixed score fidelity, whereas the evaluated broad-continuation model had higher mean Top-1 success with the same aggregate best-of-10 recovery. Focusing supervision on structurally consequential or more consistently specified corrections did not consistently…