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CataAI
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PoseX

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The dataset viewer is not available for this split.
Cannot extract the features (columns) for the split 'train' of the config 'default' of the dataset.
Error code:   FeaturesError
Exception:    ArrowInvalid
Message:      Schema at index 1 was different: 
sequences: list<item: struct<protein: struct<id: list<item: string>, sequence: string>, ligand: struct<id: string, smiles: string>>>
name: string
modelSeeds: list<item: int64>
dialect: string
version: int64
vs
sequences: list<item: struct<protein: struct<id: string, sequence: string>, ligand: struct<id: string, smiles: string>>>
name: string
modelSeeds: list<item: int64>
dialect: string
version: int64
Traceback:    Traceback (most recent call last):
                File "/src/services/worker/src/worker/job_runners/split/first_rows.py", line 231, in compute_first_rows_from_streaming_response
                  iterable_dataset = iterable_dataset._resolve_features()
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/iterable_dataset.py", line 3335, in _resolve_features
                  features = _infer_features_from_batch(self.with_format(None)._head())
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/iterable_dataset.py", line 2096, in _head
                  return next(iter(self.iter(batch_size=n)))
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/iterable_dataset.py", line 2296, in iter
                  for key, example in iterator:
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/iterable_dataset.py", line 1856, in __iter__
                  for key, pa_table in self._iter_arrow():
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/iterable_dataset.py", line 1878, in _iter_arrow
                  yield from self.ex_iterable._iter_arrow()
                File "/src/services/worker/.venv/lib/python3.9/site-packages/datasets/iterable_dataset.py", line 504, in _iter_arrow
                  yield new_key, pa.Table.from_batches(chunks_buffer)
                File "pyarrow/table.pxi", line 4116, in pyarrow.lib.Table.from_batches
                File "pyarrow/error.pxi", line 154, in pyarrow.lib.pyarrow_internal_check_status
                File "pyarrow/error.pxi", line 91, in pyarrow.lib.check_status
              pyarrow.lib.ArrowInvalid: Schema at index 1 was different: 
              sequences: list<item: struct<protein: struct<id: list<item: string>, sequence: string>, ligand: struct<id: string, smiles: string>>>
              name: string
              modelSeeds: list<item: int64>
              dialect: string
              version: int64
              vs
              sequences: list<item: struct<protein: struct<id: string, sequence: string>, ligand: struct<id: string, smiles: string>>>
              name: string
              modelSeeds: list<item: int64>
              dialect: string
              version: int64

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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.

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