PDBbind
Curated PDB complexes with experimental binding affinities — de facto standard for ML affinity prediction.
Composite
75.9
Experimental validation
Retrospective
Stages
Hit IDLead ID / ADMET
Modalities
small-moleculeprotein-general
Task types
binding-affinity
Size
complexes: 23,500
general_set: 19,443
refined_set: 5,316
general_set: 19,443
refined_set: 5,316
License
Academic-only
First release
2004
Last updated
2022-01
Official site
Leaderboard
→ leaderboard
Dataset
Code / GitHub
→ repository
HuggingFace
→ HF
Paper
The PDBbind Database: Methodologies and Updates · Wang R, Fang X, Lu Y, Wang S · 2005 · paper · doi:10.1021/jm048957q · 2,100 citations
Flags
data-leakage-known
Experts
Groups
Hosted by
Related benchmarks
Rubric (7-criterion)
rigor
4
coverage
5
maintenance
2
adoption
5
quality
3
accessibility
3
industry_relevance
4
Notes
Scaffold/temporal leakage well-documented. Pair with CASF + LeakyPDB.