---
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`.