Small Molecules
💊 Benchmarks for small-molecule drug discovery — from virtual screening through ADMET to clinical endpoints.
60
Benchmarks
83
Avg composite score
13
Wet-lab / prospective validated
11
Pipeline stages covered
Stage distribution
Virtual Cell (1)Disease Modeling (1)Target ID (3)Hit ID (30)Lead ID / ADMET (35)Developmental Candidate (8)IND-enabling (13)Post-market / RWE (3)
Validation distribution
Wet-lab confirmed (11)
Prospective (2)
Retrospective (42)
None (5)
All Small Molecules benchmarks (60)
| # | Benchmark | Stages | Validation | Score | Flags |
|---|---|---|---|---|---|
| 1 | TDC ADMET Group | Lead ID / ADMET | Retrospective | 100.0 | |
| 2 | ChEMBL | Hit IDLead ID / ADMET | Wet-lab confirmed | 97.5 | |
| 3 | PoseBusters | Hit ID | Retrospective | 97.0 | |
| 4 | PLINDER | Hit ID | Retrospective | 97.0 | |
| 5 | PLINDER v2 Protein-Ligand Benchmark | Hit ID | Retrospective | 97.0 | |
| 6 | RxRx3 Phenomics Benchmark | Hit IDLead ID / ADMET | Wet-lab confirmed | 94.9 | |
| 7 | CASP16 | Hit ID | Retrospective | 94.4 | |
| 8 | CAMEO weekly targets | Hit ID | Retrospective | 94.4 | |
| 9 | Boltz-1 Structure Prediction Benchmark | Hit ID | Retrospective | 94.4 | |
| 10 | ORD Reaction Benchmark | Developmental Candidate | Retrospective | 93.9 | |
| 11 | ASAP Discovery Antiviral 2025 | Hit IDLead ID / ADMET | Prospective | 93.9 | |
| 12 | PoseX (Protein-Ligand Docking Benchmark) | Hit IDLead ID / ADMET | Retrospective | 91.4 | leakage_preventioncross_dockingleaderboard |
| 13 | FAERS (raw) | Post-market / RWE | Retrospective | 91.1 | |
| 14 | LINCS L1000 / CMap | Virtual CellDisease ModelingTarget ID | Wet-lab confirmed | 89.9 | |
| 15 | canSAR | Target IDHit ID | Wet-lab confirmed | 89.4 | |
| 16 | Practical Molecular Optimization (PMO) | Lead ID / ADMETDevelopmental Candidate | Retrospective | 88.9 | |
| 17 | PubChem BioAssay | Hit ID | Wet-lab confirmed | 88.6 | |
| 18 | Polaris ADMET | Lead ID / ADMET | Prospective | 88.4 | |
| 19 | Cell Line Sensitivity Benchmark (CLSB) | Target IDLead ID / ADMET | Wet-lab confirmed | 88.1 | |
| 20 | ISM Benchmarks: GPCRs (Insilico) | Hit IDLead ID / ADMET | Retrospective | 87.6 | |
| 21 | ToxCast | Lead ID / ADMETIND-enabling | Retrospective | 85.6 | |
| 22 | GNNBench-Drug 2026 | Hit IDLead ID / ADMET | Retrospective | 85.6 | |
| 23 | OpenBind EV-A71 Structure-Affinity Dataset | Hit IDLead ID / ADMET | Wet-lab confirmed | 84.8 | experimental_validationcrystallography |
| 24 | CT-Open (Live Clinical Trial Outcome Benchmark) | phase-iiiphase-iphase-ii | Retrospective | 84.8 | live_benchmarkleakage_freeclinical |
| 25 | ISM Benchmarks: ADMET (Insilico) | Lead ID / ADMETIND-enabling | Wet-lab confirmed | 84.6 | |
| 26 | Longevity Compound Benchmark | Hit IDLead ID / ADMET | Wet-lab confirmed | 84.6 | |
| 27 | DMPKBench (DMPK LLM Evaluation Benchmark) | IND-enablingLead ID / ADMET | None | 83.8 | llm_benchmarkmulti_modalchinese_benchmark |
| 28 | MoleculeACE | Lead ID / ADMET | Retrospective | 83.3 | |
| 29 | BOOM (Benchmarking Out-Of-Distribution Molecular Predictions) | Hit IDLead ID / ADMET | None | 83.3 | neurips_2025ood_evaluationcritical_finding |
| 30 | OffSides / TWOSIDES | Post-market / RWE | Retrospective | 83.0 | |
| 31 | DrugComb 2.0 Synergy Benchmark | Lead ID / ADMETDevelopmental Candidate | Retrospective | 83.0 | |
| 32 | DMPK Integrated Benchmark | Lead ID / ADMETDevelopmental Candidate | Retrospective | 82.5 | |
| 33 | LSD Large-Scale Docking Database | Hit ID | Wet-lab confirmed | 82.5 | ultra_large_scaleexperimental_validation |
| 34 | BELKA (Big Encoded Library for Chemical Assessment) | Hit ID | Retrospective | 82.5 | neurips_2024kaggleultra_large_scalecompetition |
| 35 | DOCKSTRING | Hit ID | Retrospective | 81.3 | |
| 36 | LIT-PCBA | Hit ID | Retrospective | 80.8 | |
| 37 | GuacaMol | Lead ID / ADMETDevelopmental Candidate | Retrospective | 80.5 | |
| 38 | Open Systems Pharmacology / PK-Sim | phase-iIND-enabling | Retrospective | 80.3 | |
| 39 | pepADMET | IND-enablingLead ID / ADMET | Retrospective | 80.0 | biologicspeptide_therapeuticsfirst_in_class |
| 40 | ADMET-AI | Lead ID / ADMET | Retrospective | 79.5 | |
| 41 | AMES (mutagenicity) | IND-enablingLead ID / ADMET | Retrospective | 79.5 | |
| 42 | MolGenBench | Hit IDLead ID / ADMET | Retrospective | 78.2 | hit_to_leadreal_world_metrics |
| 43 | MoleculeNet | Lead ID / ADMETHit ID | Retrospective | 78.0 | data-leakage-known |
| 44 | USPTO-50K / USPTO-MIT (Retrosynthesis) | Lead ID / ADMETDevelopmental Candidate | Retrospective | 78.0 | data-leakage-known |
| 45 | Tox21 | Lead ID / ADMETIND-enabling | Retrospective | 77.5 | |
| 46 | TDC DrugSyn (OncoPolyPharm + DrugComb_NCI60) | Developmental CandidateLead ID / ADMET | Wet-lab confirmed | 77.0 | |
| 47 | Obach PK Dataset | phase-iIND-enablingLead ID / ADMET | Retrospective | 77.0 | |
| 48 | FGBench (Functional Group Molecular Property Reasoning) | Hit IDLead ID / ADMET | None | 77.0 | neurips_2025llm_benchmarkinterpretability |
| 49 | CASF-2016 | Hit ID | Retrospective | 76.2 | |
| 50 | PDBbind | Hit IDLead ID / ADMET | Retrospective | 75.9 | data-leakage-known |
| 51 | SIDER | Post-market / RWEIND-enabling | Retrospective | 74.9 | |
| 52 | Simcyp Validation Sets | phase-iphase-iiIND-enabling | Retrospective | 74.4 | license-gated-commercial |
| 53 | hERG (cardio-tox) TDC | IND-enablingLead ID / ADMET | Retrospective | 73.9 | |
| 54 | DILI / LD50 Zhu | IND-enablingLead ID / ADMET | Retrospective | 73.9 | |
| 55 | DUD-E | Hit ID | Retrospective | 72.9 | data-leakage-knowndeprecated-recommend-replace |
| 56 | MOSES | Lead ID / ADMETDevelopmental Candidate | Retrospective | 72.4 | |
| 57 | DO Challenge 2025 (DeepOrigin Autonomous Drug Discovery) | Hit ID | None | 70.9 | competitionagent_benchmark |
| 58 | VSDS-vd (Virtual Screening Decoy Set for Docking) | Hit ID | None | 65.8 | chinese_benchmarkvirtual_screening |
| 59 | ClinTox | Lead ID / ADMETIND-enabling | Retrospective | 65.6 | data-leakage-known |
| 60 | DEKOIS 2.0 | Hit ID | Retrospective | 57.5 | deprecated-recommend-replace |