| --- |
| license: other |
| license_name: bigbind |
| tags: |
| - molecular-docking |
| - gnina |
| - drug-discovery |
| - structure-based-virtual-screening |
| pretty_name: BigBind GNINA-Docked Poses |
| size_categories: |
| - 1M<n<10M |
| configs: |
| - config_name: default |
| data_files: |
| - split: train |
| path: bigbind_gnina_scores.parquet |
| --- |
| |
| # BigBind GNINA-Docked Poses |
|
|
| GNINA redocking of every protein-ligand pair in BigBind (train/val/test, including SNA |
| decoy variants). Each ligand is docked into its BigBind pocket and rescored with |
| GNINA's CNN scoring function. |
|
|
| ## Files |
|
|
| | File | Contents | |
| |---|---| |
| | `results.tar.gz` | All docked poses, one folder per protein target: `results/{protein_id}/{ligand}.sdf` | |
| | `bigbind-docked-vs/{protein_id}.tar.gz` | Same poses, re-split per target so a single protein can be fetched without downloading the whole archive | |
| | `bigbind_gnina_scores.parquet` | One row per ligand, with pose-derived score columns (below) | |
|
|
| ## Scores schema |
|
|
| | Column | Description | |
| |---|---| |
| | `protein_id` | BigBind pocket identifier | |
| | `ligand_smiles` | Ligand SMILES | |
| | `label` | 1 = active, 0 = inactive/decoy (from BigBind) | |
| | `n_poses` | Number of poses GNINA returned | |
| | `gnina_best_*` | Score at the pose GNINA's CNN rates most likely correct (`minimized_affinity`, `cnn_score`, `cnn_affinity`, `cnn_vs`, `cnn_affinity_var`) | |
| | `gnina_mean_*`, `gnina_std_*` | Mean / population std of each score across all poses | |
| | `gnina_docked_status` | Whether GNINA returned any pose for this ligand | |
| | `docked_pose_sdf_path` | Pose path relative to `results/`, e.g. `1433S_HUMAN_1_233_0/mol_4699.sdf` | |
| | `compressed_docked_pose_sdf_path` | Where to find that same pose inside `bigbind-docked-vs/`, e.g. `bigbind-docked-vs/1433S_HUMAN_1_233_0.tar.gz/results/1433S_HUMAN_1_233_0/mol_4699.sdf` | |
|
|
| Column layout follows the [Kingldore/dude-vs](https://huggingface.co/datasets/Kingldore/dude-vs) schema. |
|
|
| ## Docking parameters |
|
|
| Docked with GNINA v1.3.2 (`master:f23dd2b`), run with `--cnn_scoring rescore --exhaustiveness 8 --num_modes 9 --seed 42`. |
|
|
| ## License |
|
|
| Derived from BigBind; usage is subject to BigBind's original license terms. |
|
|
| ## Citation |
|
|
| Brocidiacono, M., Francoeur, P., Aggarwal, R., Popov, K. I., & Koes, D. R. (2024). |
| BigBind: Learning from Nonstructural Data for Structure-Based Virtual Screening. |
| *Journal of Chemical Information and Modeling*. https://doi.org/10.1021/acs.jcim.3c01211 |
|
|
