YupuZ/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
├── 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 ([email protected])
• Zhe Jiang ([email protected])