jiangteam/DecoyDB

🔧Code, 📂Dataset

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:

DecoyDB
├── README.md                                              # This file
├── complexes.csv                                          # Complex ID and paths for the data
├── data.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

The data.zip can be found in assets branch.

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 ([email protected])
• Zhe Jiang ([email protected])
• Chenglong Li ([email protected])
• Gustavo Seabra ([email protected])
• Yanjun Li ([email protected])