Datasets:

Synthyra
/

PLINDER

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:

@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.