Smina Docking
DockingPhysics-based molecular docking.
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
Binary Classification
pointwiseAUPRC0.3415
Area under the precision-recall curve. More informative when class balance is skewed.
AUROC0.6491
Area under the ROC curve. Measures discrimination ability across all thresholds.
EF 1%0.4690
Enrichment factor at 1%. How many actives found in the top 1% vs random.
EF 5%0.9381
Enrichment factor at 5%. How many actives found in the top 5% vs random.
Pairwise Ordinal
pairwisePairwise Accuracy0.5115
Fraction of pairs correctly ordered by ordinal rank.
SAR Winner (LLE)
listwisemrr0.4270
top1_accuracy0.1624
SAR Winner (Ordinal)
listwisemrr0.4490
top1_accuracy0.1813