| # CrossDocked Dataset | |
| This dataset contains protein-ligand complexes from the CrossDocked database. | |
| ## Dataset Structure | |
| ``` | |
| crossdocked/ | |
| ├── pl/ | |
| │ ├── crossdocked_v1.1_rmsd1.0_pocket10_processed_fullatom.lmdb # Main LMDB database (166,500 entries) | |
| │ ├── crossdocked_v1.1_rmsd1.0_pocket10_processed_fullatom.lmdb-lock | |
| │ ├── crossdocked_name2id.pt # Mapping from (PDB, SDF) pairs to LMDB indices | |
| │ └── split_by_name_10m.pt # Train/Val/Test split (100 test samples) | |
| └── crossdocked_test/ # Test set files (100 protein-ligand complexes) | |
| └── [protein_dirs]/ | |
| ├── *.pdb # Protein structure | |
| └── *.sdf # Ligand structure | |
| ``` | |
| ## Dataset Statistics | |
| - **Total Entries**: 166,500 protein-ligand complexes | |
| - **Test Set**: 100 complexes | |
| - **Format**: LMDB database with pickled EasyDict objects | |
| ## Data Fields | |
| Each entry in the LMDB database contains: | |
| - `protein`: Protein structure data (element, positions, backbone info, atom names, etc.) | |
| - `ligand`: Ligand molecule data (SMILES, element, positions, bonds, features, etc.) | |
| - `entry`: Metadata list | |
| - `id`: Unique identifier | |
| ## Citation | |
| If you use this dataset, please cite the original CrossDocked paper: | |
| ## License | |
| Please refer to the original CrossDocked dataset license. | |