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Datasets:
kohbanye
/
crossdocked2020

Tasks:
Other
Modalities:
Text
Formats:
webdataset
Size:
1M - 10M
Tags:
drug-discovery
molecular-generation
protein-ligand
structural-biology
Libraries:
Datasets
WebDataset
License:
Dataset card Data Studio Files
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  1. README.md +61 -0
  2. ligands/000000.tar +3 -0
  3. ligands/000001.tar +3 -0
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  37. manifest.parquet +3 -0
  38. receptors/shard-000.tar.gz +3 -0
README.md ADDED
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+ ---
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+ license: cc0-1.0
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+ task_categories:
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+ - other
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+ tags:
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+ - drug-discovery
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+ - molecular-generation
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+ - protein-ligand
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+ - structural-biology
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+ size_categories:
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+ - 1M<n<10M
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+ ---
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+
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+ # CrossDocked2020
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+
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+ Pre-processed CrossDocked2020 dataset containing raw receptor PDB and ligand
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+ SDF.gz files, organized for efficient loading.
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+
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+ ## Dataset Summary
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+
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+ - **Unique pairs**: 2,533,288
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+ - **Unique receptor PDB files**: 24,533
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+ - **Source types**: cdonly, it0, it2, it2_redocked, it2_10p20n, mod_it2,
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+ it2_completeset, it2_redocked_completeset, mod_it2_completeset
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+ - **Fold splits**: 3 folds (0, 1, 2) per source type category
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+ (completeset categories only populate fold0)
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+
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+ ## Repository Structure
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+
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+ ```
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+ receptors/ Unique receptor PDB files in tar.gz archives
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+ ligands/ Ligand SDF.gz files in tar shards (WebDataset-compatible)
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+ manifest.parquet Pair index with metadata and fold split info
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+ ```
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+
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+ ## Ligand Tar Shard Format
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+
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+ Each shard is a tar file containing pairs of files per sample:
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+ - `{pair_idx:07d}.sdf.gz` — original ligand SDF.gz (all conformers)
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+ - `{pair_idx:07d}.json` — metadata (receptor_path, complex_dir, source_type)
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+
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+ ## Manifest Schema
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+
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+ | Column | Type | Description |
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+ |--------|------|-------------|
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+ | pair_idx | uint32 | Global unique pair ID |
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+ | complex_dir | string | Complex directory name |
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+ | receptor_pdb | string | Receptor PDB filename |
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+ | ligand_sdf_gz | string | Ligand SDF.gz filename |
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+ | source_type | string | One of 9 categories (see Source types above) |
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+ | shard_idx | uint16 | Ligand shard number |
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+ | label | int8 | Types file label (0/1) |
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+ | score1 | float32 | Types file score 1 |
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+ | score2 | float32 | Types file score 2 |
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+ | {cat}_fold{n} | string | "train" / "test" per category and fold |
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+
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+ ## Original Source
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+
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+ Paul G. Francoeur, Tomohide Masuda, Jocelyn Sunseri, Andrew Jia,
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+ Richard B. Iovanisci, Ian Snyder, David R. Koes.
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+ *J. Chem. Inf. Model.* 2020, 60(9), p.4200-4215.
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