DockM8_v1.1_DUD-E_benchmarking_data

DockM8 — DUD-E benchmark data============================== This repository contains benchmarking data for the DUD-E (Directoryof Useful Decoys, Enhanced) dataset produced with DockM8 v1.1. It isintended for benchmarking scoring functions and machine-learningmodels, and as a large archive of pre-docked poses generated bymultiple docking algorithms. Single download: DUD-E.tar.bz2 Archive layout (nested compression)----------------------------------- The files are NOT directly browsable — the Zenodo download is acompressed archive of compressed archives of gzipped SDFs. You mustuse the `extract_zenodo.py` helper from the DockM8 repository tounpack them. DUD-E.tar.bz2 # outer archive (Zenodo download)└── phase2/ └── [target_name].tar.bz2 # one inner archive per DUD-E target └── [target_name]/ ├── [target]_activity_data.csv # experimental binding data ├── [target]_docking_library.sdf # compounds to dock ├── [target]_ligand.sdf # reference ligand(s) ├── [target]_pocket.pdb # binding-site definition ├── [target]_pocket.pdbqt # binding site (AutoDock format) ├── [target]_protein.pdb # original structure ├── [target]_protein_prepared.pdb # prepared for docking └── results/ ├── allposes.sdf.gz # combined poses (gzipped) ├── allposes_rescored.csv # scores for all poses ├── [target]_prepared_library.sdf.gz ├── [docking_program]/ # per-engine outputs │ ├── [program]_poses.sdf.gz # raw poses (gzipped) │ └── [program]_poses_rescored.sdf.gz ├── performance/ │ └── [target]_[program]_[pose_selection]_performance.csv ├── scores/ │ └── [target]_[program]_[pose_selection]_scores.csv └── clustering/ └── [target]_[program]_[pose_selection]_selected_poses.sdf.gz How to extract-------------- Clone the DockM8 repo (main branch) and run the helper script — itreverses all three compression layers in one command: git clone https://github.com/DrugBud-Suite/DockM8.git cd DockM8 # Put the downloaded archive in a folder, then: python -m analysis.extract_zenodo /path/to/downloads /path/to/output \ --archives DUD-E.tar.bz2 The script will: 1. Extract the outer .tar.bz2, 2. Extract each per-target inner .tar.bz2, 3. Decompress every *.sdf.gz in place. Output layout: /path/to/output/DUD-E/<targets> IMPORTANT: Do NOT attempt manual extraction with `tar -xjf` alone —you will be left with nested tarballs and thousands of unreadable.sdf.gz files. Always use the helper script.