Benchmarks

Validated Benchmarks

Transparent, reproducible scoring performance on public benchmark datasets. All profiles are validated with fixed random seeds.

Property-matched decoy benchmarks (Vogel et al., J Chem Inf Model 2011)

Target	Class	AUC	Actives	Status	Profile
MDM2 E3 Ubiquitin Ligase (PDB: 3LBK)	PPI	0.855	40	GOLD	`mdm2_dekois2_ppi_gold_v3`
HSP90 Heat Shock Protein 90	Chaperone	0.815	40	GOLD	`hsp90_dekois2_gold_v2`
AmpC Beta-Lactamase	Enzyme	0.815	48	GOLD	`ampc_gold_v1`
Factor Xa Coagulation Factor Xa	Protease	0.800	39	GOLD	`fxa_dekois2_gold_v2`
ACE Angiotensin Converting Enzyme	Metalloprotease	0.825	40	PROMOTED	`ace_metal_v5`
PARP1 Poly(ADP-Ribose) Polymerase 1	Enzyme	0.747	40	PROMOTED	`hbq_parp1_tuned_v2`
CDK2 Cyclin-Dependent Kinase 2	Kinase	0.692	40	CANDIDATE	`hbq_cdk2_hinge_v1`

All benchmarks run with fixed random seeds (42, 1, 2, 3) for full reproducibility. Results show mean AUC across seeds.

Property-matched decoys that prevent trivial discrimination based on molecular weight or LogP differences.

All results from LZ Dock 2.0 native docking with Rust-accelerated genetic algorithm search.