README.md

---
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)