|
|
--- |
|
|
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`. |
|
|
|
