Deterministic molecular docking using Smina (a fork of AutoDock Vina). Ligands are docked into the known protein binding site and scored by a physics-based energy function. Uses the reference crystal structure from PDB.
Design Rationale
Docking represents the gold standard of physics-based virtual screening. Strong performance here would validate the benchmark's structural relevance.
Evaluation Scores
Area under the precision-recall curve. More informative when class balance is skewed.
Area under the ROC curve. Measures discrimination ability across all thresholds.
Enrichment factor at 1%. How many actives found in the top 1% vs random.
Enrichment factor at 5%. How many actives found in the top 5% vs random.
Fraction within ±1 rank of the true rank. Reflects triage decisions.
Harrell's C statistic — probability that a random pair is correctly ordered.
Rank correlation averaged within assay groups.
Fraction of predictions matching the exact ordinal rank.
Fraction of pairs correctly ordered by ordinal rank.