arXiv Machine Learning October 15, 2026 By Gor Simonyan, Tatevik Abrahamyan, Narek Abelyan, Tigran Fahradyan, Hrant Khachatrian

PMO-Dock: Benchmarking Docking, Specificity, and Generalization in Molecular Optimization

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PMO-Dock introduces a standardized benchmark for docking‑based molecular optimization, comprising 25 tasks that span hit generation, lead optimization, and a specificity task that rewards strong on‑target binding while penalizing off‑target interactions. The protocol separates model development from final evaluation, using validation tasks for hyperparameter tuning and held‑out test tasks evaluated under a strict oracle budget to mimic realistic drug‑discovery constraints. Four diverse methods—Saturn, GenMol, Genetic‑guided GFlowNet, and ChemLlama—were benchmarked, revealing no single method dominates across all tasks and highlighting limited hyperparameter transferability, which underscores the need for method‑dependent selection strategies.

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