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README.md

@@ -39,16 +39,11 @@ dataset_info:
     dtype: int32
   splits:
   - name: train
-    num_bytes: 75872160
     num_examples: 418381
   - name: valid
-    num_bytes: 196539
     num_examples: 1157
   - name: test
-    num_bytes: 233913
     num_examples: 1436
-  download_size: 10189662
-  dataset_size: 76302612
 configs:
 - config_name: default
   data_files:
@@ -59,3 +54,55 @@ configs:
   - 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`.