README.md

metadata

license: cc0-1.0
task_categories:
  - other
tags:
  - drug-discovery
  - molecular-generation
  - protein-ligand
  - structural-biology
size_categories:
  - 1M<n<10M

CrossDocked2020

Pre-processed CrossDocked2020 dataset containing raw receptor PDB and ligand SDF.gz files, organized for efficient loading.

Dataset Summary

• Unique pairs: 2,533,288
• Unique receptor PDB files: 24,533
• Source types: cdonly, it0, it2, it2_redocked, it2_10p20n, mod_it2, it2_completeset, it2_redocked_completeset, mod_it2_completeset
• Fold splits: 3 folds (0, 1, 2) per source type category (completeset categories only populate fold0)

Pose Counts

Each ligand .sdf.gz contains multiple docked poses concatenated as SDF records. The 5 filename patterns correspond to different gnina iterations (tt_min is the energy-minimized crystal pose; the others are docked poses from successive scoring iterations). Pose totals across the 2,533,288 uploaded files:

Filename pattern	Files	Poses	Mean poses/file
tt_docked	594,185	11,394,561	19.18
it1_tt_docked	585,876	11,235,334	19.18
it2_tt_docked	415,654	8,050,604	19.37
it1_it2_tt_docked	339,656	6,672,859	19.65
tt_min	597,917	597,917	1.00
Total	2,533,288	37,951,275	14.98

So the dataset holds 37,951,275 poses distributed across 2,533,288 .sdf.gz files (≈ 38.0 M poses).

Repository Structure

receptors/          Unique receptor PDB files in tar.gz archives
ligands/            Ligand SDF.gz files in tar shards (WebDataset-compatible)
manifest.parquet    Pair index with metadata and fold split info

Ligand Tar Shard Format

Each shard is a tar file containing pairs of files per sample:

• {pair_idx:07d}.sdf.gz — original ligand SDF.gz (all conformers)
• {pair_idx:07d}.json — metadata (receptor_path, complex_dir, source_type)

Manifest Schema

Column	Type	Description
pair_idx	uint32	Global unique pair ID
complex_dir	string	Complex directory name
receptor_pdb	string	Receptor PDB filename
ligand_sdf_gz	string	Ligand SDF.gz filename
source_type	string	One of 9 categories (see Source types above)
shard_idx	uint16	Ligand shard number
label	int8	Types file label (0/1)
score1	float32	Types file score 1
score2	float32	Types file score 2
{cat}_fold{n}	string	"train" / "test" per category and fold

Original Source

Paul G. Francoeur, Tomohide Masuda, Jocelyn Sunseri, Andrew Jia, Richard B. Iovanisci, Ian Snyder, David R. Koes. J. Chem. Inf. Model. 2020, 60(9), p.4200-4215.