Update README.md

README.md

@@ -1,3 +1,57 @@
----
-license: apache-2.0
----
+---
+task_categories:
+- feature-extraction
+language:
+- en
+tags:
+- biology
+- chemistry
+- drug
+license: apache-2.0
+size_categories:
+- 1M<n<10M
+---
+🔧[Code](https://github.com/spatialdatasciencegroup/Decoy_DB), 📂[Dataset](https://huggingface.co/datasets/YupuZ/DecoyDB)
+## Dataset Summary
+DecoyDB is a curated dataset of high-resolution protein-ligand complexes and their associated decoy structures. It is designed to support research on graph contrastive learning, binding affinity prediction, and structure-based drug discovery. The dataset is derived from experimentally resolved complexes and refined to ensure data quality.
+
+## Data Structure
+Each protein-ligand complex is stored in a nested directory under DecoyDB/, using the format:
+```plaintext
+DecoyDB
+├── README.md                                              # This file
+├── merged_decoy_scores.csv                                # RMSD and Vina score for all decoys
+├── structures.zip                                         # Structures for proteins, ligands and decoys
+  ├── {prefix}/                                            # {prefix} = first 2 characters of the complex ID (e.g., '1A', '2B')
+  │   └── {complex_id}/                                    # Unique identifier for each complex (e.g., 1A2C_H1Q)
+  │       ├── {complex_id}_ligand.pdbqt                    # Ligand structure in AutoDock format
+  │       ├── {complex_id}_target.pdbqt                    # Protein structure in AutoDock format
+  │       ├── {complex_id}_decoys.pdbqt                    # Concatenated decoy structures
+  │       └── {complex_id}_decoys_scores.csv               # Corresponding RMSD scores for each decoy
+```
+## Dataset Details
+### Dataset Refinement
+To construct DecoyDB, we first filtered protein–ligand complexes from the Protein Data Bank (PDB) with a resolution ≤ 2.5 Å and applied the following refinement steps:
+
+- Removed ligands with molecular weights outside the (50, 1000) range.
+- Excluded complexes involving metal clusters, monoatomic ions, and common crystallization molecules.
+- Retained ligands with elements limited to C, N, O, H, S, P, and halogens.
+- Retained those protein chains with at least one atom within 10 Å of the ligand.
+- Saved the ligand and protein separately.
+
+### Decoy Generation
+
+For each refined protein–ligand complex, **100 decoy poses** were generated using **AutoDock Vina 1.2**, with a 5 Å padding grid box and an exhaustiveness parameter of 8 and remove unrealistic generated structures.
+
+## Dataset Statistics
+
+- Number of protein–ligand complexes: **61,104**
+- Number of decoys: **5,353,307**
+- Average number of decoys per complex: **88**
+- Average RMSD: **7.22 Å**
+- RMSD range: **[0.03, 25.56] Å**
+
+## Contact
+
+- Yupu Zhang (y.zhang1@ufl.edu)
+- Zhe Jiang (zhe.jiang@ufl.edu)