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.