| --- |
| 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) |
