PocketVina Atlas
Approved drugs docked into the predicted pockets of the human AlphaFold proteome.
Akalin Lab · Max Delbrück Center
18,713 proteins · 3,108 compounds · 71.3 M pairs · 6.6 B poses
Every compound is docked into the five top-ranked predicted pockets of each protein.
Browse
Proteins by class
18,713proteins
By ChEMBL protein class, each protein with its pockets and docked drugs.
Drugs by ATC class
3,108compounds
By ATC class (from ChEMBL), each drug with its results across the proteome.
Random pair
71.3 Mpairs
Pick a random protein and drug and see how well it docks.
Downloads
≈2.5 TBbulk release
Tables (Parquet, DuckDB), every pose, and checksums; single poses on each pair.
Example complexes
How to use the atlas
- Search a protein by gene symbol, UniProt, Ensembl or Entrez ID, or a drug by name or ChEMBL ID. An atlas ID of a pocket, pair or pose opens it, for example
P00519_PVL00129(imatinib on ABL1). Press / on any page to search. - Explore a protein: pick a compound and see its pose in each pocket in 3D, with scores, contacts and PoseBusters checks.
- Download single poses, your selection as a ZIP, or the whole release (Parquet + DuckDB). Downloads
Release
Release v1.1 · built · docked with PocketVina
| Number | Value | Definition |
|---|---|---|
| Proteins | 18,713 | Human proteins with docking results: AlphaFold DB v6 models, one per UniProt accession. |
| Compounds | 3,108 | Catalogue entries of the approved-drug library (Selleck) used as input. |
| unique drug molecules | 2,559 | PVL IDs (docked structures) with results whose docked structure is the drug molecule. |
| Protein × compound pairs | 71,289,971 | All protein × compound pairs with a docking result: every catalogue entry, both forms of salt entries and non-drug entries included. |
| library entries as screened | 56,450,562 | Protein × compound pairs of the library entries as screened: one per protein and catalogue number. |
| desalted forms of salt entries | 14,839,409 | Protein × compound pairs of the desalted forms of salt entries. |
| unique protein × molecule pairs | 48,406,051 | Each protein and unique docked molecule counted once (catalogue entries with the same structure count once). |
| Pocket runs | 341,234,334 | Docking runs, one per pair and pocket (up to 5 pockets per protein), over all catalogue numbers. |
| Poses | 6,594,897,025 | Docked poses (Vina modes) with scores over all pocket runs. |
| library entries as screened | 5,193,646,087 | Docked poses (Vina modes) of the library entries as screened. |
| desalted forms of salt entries | 1,401,250,938 | Docked poses (Vina modes) of the desalted forms of salt entries. |
Every number with its definition and source: About · Numbers.
Built with PocketVina
PocketVina docks each compound in several predicted pockets of a protein instead of one guessed site, and every pose in the atlas comes from it.
Cite
Sarigun A, Uyar B, Franke V, Akalin A. PocketVina Enables Scalable and Highly Accurate Physically Valid Docking through Multi-Pocket Conditioning. arXiv:2506.20043 (2025).