| --- |
| dataset_info: |
| features: |
| - name: system_id |
| dtype: string |
| - name: split |
| dtype: string |
| - name: entry_pdb_id |
| dtype: string |
| - name: entry_determination_method |
| dtype: string |
| - name: entry_resolution |
| dtype: float32 |
| - name: is_experimental |
| dtype: bool |
| - name: protein_sequence |
| dtype: string |
| - name: protein_chain_id |
| dtype: string |
| - name: protein_instance_chain |
| dtype: string |
| - name: ligand_smiles |
| dtype: string |
| - name: ligand_ccd_code |
| dtype: string |
| - name: ligand_instance_chain |
| dtype: string |
| - name: ligand_is_proper |
| dtype: bool |
| - name: ligand_is_covalent |
| dtype: bool |
| - name: ligand_molecular_weight |
| dtype: float32 |
| - name: system_pass_validation_criteria |
| dtype: bool |
| - name: system_num_protein_chains |
| dtype: int32 |
| - name: system_num_ligand_chains |
| dtype: int32 |
| splits: |
| - name: train |
| num_examples: 425694 |
| - name: valid |
| num_examples: 1065 |
| - name: test |
| num_examples: 1311 |
| configs: |
| - config_name: default |
| data_files: |
| - split: train |
| path: data/train-* |
| - split: valid |
| path: data/valid-* |
| - split: test |
| path: data/test-* |
| --- |
| |
| # PLINDER Protein-Ligand Interactions |
|
|
| This dataset contains per-ligand, per-interacting-protein-chain pairs from the PLINDER dataset. |
| Splits follow the official stringent train/val/test split provided by PLINDER (val is renamed to valid on the Hub). |
|
|
| ## Row Schema |
|
|
| | Column | Type | Description | |
| |--------|------|-------------| |
| | `system_id` | string | PLINDER system ID | |
| | `split` | string | Dataset split (train/valid/test) | |
| | `entry_pdb_id` | string | PDB entry ID | |
| | `entry_determination_method` | string | Experimental method (X-RAY DIFFRACTION, CRYO-EM, NMR, etc.) | |
| | `entry_resolution` | float | Structure resolution in Angstroms | |
| | `is_experimental` | bool | Whether the structure is experimentally determined (always True for PLINDER) | |
| | `protein_sequence` | string | Amino acid sequence of the interacting protein chain | |
| | `protein_chain_id` | string | Protein chain identifier | |
| | `protein_instance_chain` | string | Full instance.chain identifier | |
| | `ligand_smiles` | string | Canonical SMILES of the ligand | |
| | `ligand_ccd_code` | string | PDB Chemical Component Dictionary code | |
| | `ligand_instance_chain` | string | Ligand instance.chain identifier | |
| | `ligand_is_proper` | bool | True if ligand is not an ion or artifact | |
| | `ligand_is_covalent` | bool | True if ligand is covalently bound | |
| | `ligand_molecular_weight` | float | Molecular weight of the ligand | |
| | `system_pass_validation_criteria` | bool | True if system passes PLINDER quality criteria | |
| | `system_num_protein_chains` | int | Number of protein chains in the system | |
| | `system_num_ligand_chains` | int | Number of ligand chains in the system | |
|
|
| ## Data Source |
|
|
| All data is derived from the Protein Data Bank (PDB) via the PLINDER dataset. |
| The `entry_determination_method` column indicates the experimental technique used: |
| - **X-RAY DIFFRACTION**: Crystal structures |
| - **CRYO-EM**: Cryo-electron microscopy structures |
| - **NMR**: Nuclear magnetic resonance structures |
| - **ELECTRON MICROSCOPY**: Other EM methods |
|
|
| ## Citation |
|
|
| If you use this dataset, please cite the PLINDER paper: |
|
|
| ```bibtex |
| @article{Durairaj2024, |
| title = {PLINDER: The Protein-Ligand Interactions Dataset and Evaluation Resource}, |
| year = {2024}, |
| journal = {bioRxiv}, |
| doi = {10.1101/2024.07.17.603955} |
| } |
| ``` |
|
|
| Generated by `Synthyra/PLINDER`. |
|
|
