README.md

metadata

license: cc-by-4.0
size_categories:
  - 1K<n<10K
language:
  - en
tags:
  - biology
configs:
  - config_name: benchmark
    data_files:
      - split: test
        path:
          - astex_benchmark.csv
          - posex_self_dock_benchmark.csv
          - posex_cross_dock_benchmark.csv

The file posex_set.zip contains processed dataset for docking evaluation, while posex_cif.zip contains the raw CIF files from RCSB PDB. For information about creating a dataset from scratch, please refer to the data construction code.
The processed dataset comprises three sub-datasets in total:

• The Astex Diverse set was curated by Hartshorn et al. [1] and contains 85 cases, it was reprocessed to adapt to our evaluation process.
• The PoseX Self-Docking set was curated by us using the PDB and contains 718 cases.
• The PoseX Cross-Docking set was curated by us using the PDB and contains 1312 pairs.

For each protein-ligand complex, there is one folder named after the PDB identifier and the CCD identifier (PDB_CCD).

Each folder contains the following files:

1. PDB file PDB_CCD_protein.pdb: The protein structure without the ligand, without solvents, and with all cofactors.
2. SDF file PDB_CCD_ligands.sdf: All instances of the ligand.
3. SDF file PDB_CCD_ligand.sdf: One instance of the ligand.
4. SDF file PDB_CCD_ligand_start_conf.sdf: One generated molecule conformation for the ligand.
5. JSON file PDB_CCD.json: Input JSON file for AlphaFold 3
6. PDB file PDB_CCD_ref_protein.pdb (unique to Cross-Docking set): The reference protein structure.
7. TXT file group_id.txt (unique to Cross-Docking set): Group information
8. In folder posex_self_docking_set and posex_cross_docking_set, a csv file named qtm.csv contains pocket structure similarity which is calculated for each evaluation data point relative to the training data.

The folder structure is:

  posex_set/
  ├── astex_diverse_set/
  │   ├── 2BSM_BSM/
  │   │   ├── 2BSM_BSM_ligand_start_conf.sdf
  │   │   ├── 2BSM_BSM_ligand.sdf
  │   │   ├── 2BSM_BSM_ligands.sdf
  │   │   ├── 2BSM_BSM_protein.sdf
  │   │   └── 2BSM_BSM.json
  │   └── ...
  ├── posex_self_docking_set/
  │   ├── 5S9U_FAD/
  │   │   ├── 5S9U_FAD_ligand_start_conf.sdf
  │   │   ├── 5S9U_FAD_ligand.sdf
  │   │   ├── 5S9U_FAD_ligands.sdf
  │   │   ├── 5S9U_FAD_protein.pdb
  │   │   └── 5S9U_FAD.json
  │   ├── qtm.csv
  │   └── ...
  ├── posex_cross_docking_set/
  │   ├── 5SAU_1IJ/
  │   │   ├── 5SAU_1IJ_ligand_start_conf.sdf
  │   │   ├── 5SAU_1IJ_ligand.sdf
  │   │   ├── 5SAU_1IJ_ligands.sdf
  │   │   ├── 5SAU_1IJ_protein.pdb
  │   │   ├── 5SAU_1IJ_ref_protein.pdb
  │   │   ├── 5SAU_1IJ.json
  │   │   └── group_id.txt
  │   ├── qtm.csv
  └── └── ...

This dataset is associated with the following paper:

@misc{jiang2025posexaidefeatsphysics,
      title={PoseX: AI Defeats Physics Approaches on Protein-Ligand Cross Docking}, 
      author={Yize Jiang and Xinze Li and Yuanyuan Zhang and Jin Han and Youjun Xu and Ayush Pandit and Zaixi Zhang and Mengdi Wang and Mengyang Wang and Chong Liu and Guang Yang and Yejin Choi and Wu-Jun Li and Tianfan Fu and Fang Wu and Junhong Liu},
      year={2025},
      eprint={2505.01700},
      archivePrefix={arXiv},
      primaryClass={cs.LG},
      url={https://arxiv.org/abs/2505.01700}, 
}

References:

[1] Hartshorn MJ, Verdonk ML, Chessari G, Brewerton SC, Mooij WTM, Mortenson PN, et al. Diverse, high-quality test set for the validation of protein-ligand docking performance. J Med Chem. 2007 Feb 1;50(4):726–41.