Datasets:
sdf.gz unknown | json dict | __key__ stringlengths 7 7 | __url__ stringclasses 2
values |
|---|---|---|---|
[
95,
95,
50,
98,
113,
48,
95,
65,
95,
114,
101,
99,
95,
53,
102,
55,
52,
95,
97,
109,
112,
95,
108,
105,
103,
95,
105,
116,
49,
95,
105,
116,
50,
95,
100,
111,
99,
107,
101,
100,
46,
112,
100,
98,
10,
10,
10,
32,
50,
57... | {
"complex_dir": "1433B_HUMAN_1_240_pep_0",
"ligand_original_name": "2bq0_A_rec_5f74_amp_lig_it1_it2_tt_docked.sdf.gz",
"pair_idx": 0,
"receptor_path": "1433B_HUMAN_1_240_pep_0/2bq0_A_rec.pdb",
"source_type": "cdonly"
} | 0000000 | hf://datasets/kohbanye/crossdocked2020@8ebfdebbe2b2118fdf123b1e092054fb307c9c93/ligands/000000.tar |
[
95,
95,
50,
98,
113,
48,
95,
65,
95,
114,
101,
99,
95,
53,
102,
55,
52,
95,
97,
109,
112,
95,
108,
105,
103,
95,
105,
116,
49,
95,
100,
111,
99,
107,
101,
100,
46,
112,
100,
98,
10,
10,
10,
32,
50,
57,
32,
51,
49,
32,
... | {
"complex_dir": "1433B_HUMAN_1_240_pep_0",
"ligand_original_name": "2bq0_A_rec_5f74_amp_lig_it1_tt_docked.sdf.gz",
"pair_idx": 1,
"receptor_path": "1433B_HUMAN_1_240_pep_0/2bq0_A_rec.pdb",
"source_type": "cdonly"
} | 0000001 | hf://datasets/kohbanye/crossdocked2020@8ebfdebbe2b2118fdf123b1e092054fb307c9c93/ligands/000000.tar |
"X18yYnEwX0FfcmVjXzVmNzRfYW1wX2xpZ19pdDJfZG9ja2VkLnBkYgoKCiAyOSAzMSAgMCAgMCAgMCAgMCAgMCAgMCAgMCAgMDk(...TRUNCATED) | {"complex_dir":"1433B_HUMAN_1_240_pep_0","ligand_original_name":"2bq0_A_rec_5f74_amp_lig_it2_tt_dock(...TRUNCATED) | 0000002 | hf://datasets/kohbanye/crossdocked2020@8ebfdebbe2b2118fdf123b1e092054fb307c9c93/ligands/000000.tar |
"X18yYnEwX0FfcmVjXzVmNzRfYW1wX2xpZ19kb2NrZWQucGRiCgoKIDI5IDMxICAwICAwICAwICAwICAwICAwICAwICAwOTk5IFY(...TRUNCATED) | {"complex_dir":"1433B_HUMAN_1_240_pep_0","ligand_original_name":"2bq0_A_rec_5f74_amp_lig_tt_docked.s(...TRUNCATED) | 0000003 | hf://datasets/kohbanye/crossdocked2020@8ebfdebbe2b2118fdf123b1e092054fb307c9c93/ligands/000000.tar |
"X18yYnEwX0FfcmVjXzVmNzRfYW1wX2xpZ19taW4ucGRiCgoKIDI5IDMxICAwICAwICAwICAwICAwICAwICAwICAwOTk5IFYyMDA(...TRUNCATED) | {"complex_dir":"1433B_HUMAN_1_240_pep_0","ligand_original_name":"2bq0_A_rec_5f74_amp_lig_tt_min.sdf.(...TRUNCATED) | 0000004 | hf://datasets/kohbanye/crossdocked2020@8ebfdebbe2b2118fdf123b1e092054fb307c9c93/ligands/000000.tar |
"X181Zjc0X0FfcmVjXzVmNzRfYW1wX2xpZ19pdDFfaXQyX2RvY2tlZC5wZGIKCgogMjkgMzEgIDAgIDAgIDAgIDAgIDAgIDAgIDA(...TRUNCATED) | {"complex_dir":"1433B_HUMAN_1_240_pep_0","ligand_original_name":"5f74_A_rec_5f74_amp_lig_it1_it2_tt_(...TRUNCATED) | 0000005 | hf://datasets/kohbanye/crossdocked2020@8ebfdebbe2b2118fdf123b1e092054fb307c9c93/ligands/000000.tar |
"X181Zjc0X0FfcmVjXzVmNzRfYW1wX2xpZ19pdDFfZG9ja2VkLnBkYgoKCiAyOSAzMSAgMCAgMCAgMCAgMCAgMCAgMCAgMCAgMDk(...TRUNCATED) | {"complex_dir":"1433B_HUMAN_1_240_pep_0","ligand_original_name":"5f74_A_rec_5f74_amp_lig_it1_tt_dock(...TRUNCATED) | 0000006 | hf://datasets/kohbanye/crossdocked2020@8ebfdebbe2b2118fdf123b1e092054fb307c9c93/ligands/000000.tar |
"X181Zjc0X0FfcmVjXzVmNzRfYW1wX2xpZ19pdDJfZG9ja2VkLnBkYgoKCiAyOSAzMSAgMCAgMCAgMCAgMCAgMCAgMCAgMCAgMDk(...TRUNCATED) | {"complex_dir":"1433B_HUMAN_1_240_pep_0","ligand_original_name":"5f74_A_rec_5f74_amp_lig_it2_tt_dock(...TRUNCATED) | 0000007 | hf://datasets/kohbanye/crossdocked2020@8ebfdebbe2b2118fdf123b1e092054fb307c9c93/ligands/000000.tar |
"X181Zjc0X0FfcmVjXzVmNzRfYW1wX2xpZ19kb2NrZWQucGRiCgoKIDI5IDMxICAwICAwICAwICAwICAwICAwICAwICAwOTk5IFY(...TRUNCATED) | {"complex_dir":"1433B_HUMAN_1_240_pep_0","ligand_original_name":"5f74_A_rec_5f74_amp_lig_tt_docked.s(...TRUNCATED) | 0000008 | hf://datasets/kohbanye/crossdocked2020@8ebfdebbe2b2118fdf123b1e092054fb307c9c93/ligands/000000.tar |
"X181Zjc0X0FfcmVjXzVmNzRfYW1wX2xpZ19taW4ucGRiCgoKIDI5IDMxICAwICAwICAwICAwICAwICAwICAwICAwOTk5IFYyMDA(...TRUNCATED) | {"complex_dir":"1433B_HUMAN_1_240_pep_0","ligand_original_name":"5f74_A_rec_5f74_amp_lig_tt_min.sdf.(...TRUNCATED) | 0000009 | hf://datasets/kohbanye/crossdocked2020@8ebfdebbe2b2118fdf123b1e092054fb307c9c93/ligands/000000.tar |
End of preview. Expand in Data Studio
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.
- Downloads last month
- 370