diffdock
Predicts protein-small-molecule binding poses with DiffDock and DiffDock-L from PDB or sequence plus SMILES/SDF/MOL2. Covers batch docking, pose triage, confidence interpretation, and validation. Use for molecular docking and virtual-screening pose generation, not binding-affinity prediction.
- Version
- 1.6
- License
- MIT license
- Compatibility
- Requires the upstream DiffDock v1.1.3 repository/environment (Python 3.9.18, PyTorch 1.13.1, fair-esm 2.0.0, RDKit/PyG) or its Docker image. Network and disk space for model weights; CUDA required by upstream sequence-folding path. Bundled CSV helper needs pandas and RDKit.
Pinned to revision 68105dd992f1, so it is the text this page describes rather than whatever the author pushed since.
Pre-approved tools experimental
Experimental field. Support varies between clients, so this list is what the author declared, not what your client will enforce.
- Read
- Write
- Edit
- Bash
- Glob
- Grep
Files
- skills/diffdock/SKILL.md
- skills/diffdock/SKILL_CN.md
- skills/diffdock/assets/batch_template.csv
- skills/diffdock/assets/custom_inference_config.yaml
- skills/diffdock/references/confidence_and_limitations.md
- skills/diffdock/references/parameters_reference.md
- skills/diffdock/references/workflows_examples.md
- skills/diffdock/scripts/analyze_results.py
- skills/diffdock/scripts/prepare_batch_csv.py
- skills/diffdock/scripts/setup_check.py
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