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---
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`.
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