Downloads

Three ways to take the data: single files on every protein page (Downloads section); your selection as ZIP, CSV or a download script (tick pairs in any table); and the bulk release below.

Bulk release

Release v1.1. Exact sizes; checksums in MANIFEST.json.

File	Content	Size
`tables/compound_entries.parquet`	Every catalogue number of the library: docked structure (PVL), what was docked, desalted entries	430 KB
`tables/compound_entries_annotated.parquet`	Catalogue numbers with names, ChEMBL IDs, ATC classes and synonyms	354 KB
`tables/compounds.parquet`	Ligand IDs (PVL): one per docked structure, with its SMILES and InChIKey	196 KB
`tables/modes.parquet`	Every Vina mode: affinity, RMSD bounds, byte position of its pose	35.8 GB
`tables/open_targets.parquet`	Open Targets diseases of each protein	1.7 MB
`tables/pair_pvl.parquet`	Protein-ligand pairs: the canonical run of each pair	54.6 MB
`tables/pairs_by_compound.parquet`	Pair results sorted by compound: highest affinity, pocket, mode, PoseBusters, ChEMBL evidence	3.3 GB
`tables/pairs_by_protein.parquet`	The same pair results sorted by protein	3.2 GB
`tables/pocket_runs.parquet`	One row per pair and pocket: best affinity, number of modes, byte position of the mode block	13.5 GB
`tables/pockets.parquet`	P2Rank pockets of each protein: score, probability, centre, residues	3.0 MB
`tables/posebusters.parquet`	PoseBusters checks of each highest-affinity pose	55.1 MB
`tables/proteins.parquet`	Proteins: identifiers, names, classes, model quality	3.7 MB
`tables/pvl_flags.parquet`	ChEMBL evidence flags per protein and ligand ID	46 KB
`tables/replicate_runs.parquet`	Pairs docked again under another catalogue number of the same structure (kept, not shown)	48.3 MB
`poses/`	One PVATLAS1 pose file per protein: highest-affinity poses and all modes of each pocket run	1.83 TB
`poses_redock/`	One PVATLAS1 pose file per protein for the desalted forms of salt entries	601.2 GB

Step by step, with a Python reader of the pose files and commands for PyMOL, ChimeraX and Jupyter: Download and visualise.

To read these files from Python, use the PocketVina package: see Python package.

One pose without downloading the whole file

Every protein has one pose file, poses/<UniProt>.poses (and poses_redock/<UniProt>.poses for the desalted forms of salt entries). The protein's table, proteins/<UniProt>.json.gz, gives the byte offset and length of each row's highest-affinity pose (columns top_off, top_len; column pf names the file). One HTTP range request returns one gzip member:

# top_off and top_len of a row of https://bimsbstatic.mdc-berlin.de/akalin/asarigun/pocketvina_atlas/data/v1.1/proteins/P00519.json.gz
curl -r <top_off>-<top_off+top_len-1> https://bimsbstatic.mdc-berlin.de/akalin/asarigun/pocketvina_atlas/data/v1.1/poses/P00519.poses | gunzip > pose.sdf

The mode blocks (all poses of one pocket run) are found the same way through the file's table B; the format is described in MANIFEST.json and the table modes.parquet lists every mode with its byte position.

Query the tables without downloading them

duckdb -c "SELECT uniprot, catalog_id, vina, best_pocket, pb_status
           FROM 'https://bimsbstatic.mdc-berlin.de/akalin/asarigun/pocketvina_atlas/data/v1.1/tables/pairs_by_compound.parquet'
           WHERE catalog_id = 'S1026' AND pb_status = 'valid'
           ORDER BY vina LIMIT 20"

Verify

MANIFEST.json in the release folder lists every file with its size and SHA-256.

Licence

The atlas's own results (poses, scores, pockets and PoseBusters checks) are under the MIT licence (text below). Data from other resources keeps its licence: AlphaFold DB models (CC BY 4.0), UniProt names and annotation (CC BY 4.0), ChEMBL data, including the evidence flags derived from it (CC BY-SA 3.0), and Open Targets diseases (CC0 1.0). The compound names and SMILES come from the vendor library; their redistribution terms are being checked.

MIT License

Copyright (c) 2026 Akalin Lab, Max Delbrück Center

Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:

The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.

THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.