README.md

metadata

license: cc-by-4.0
size_categories:
  - 1K<n<10K

The 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/
  ├── 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
  └── └── ...

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.