Individual skill
molecular-docking
End-to-end molecular docking pipeline. Target preparation, pocket detection, protein-ligand docking (DiffDock/Vina), scoring, interaction analysis, and pose ranking.
backend/cli/skills/chemistry/molecular-docking/SKILL.md
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# Molecular Docking Pipeline
## Overview
This skill provides a complete end-to-end molecular docking workflow covering every stage from raw protein structure to ranked, annotated binding poses. It integrates classical physics-based docking (AutoDock Vina) with modern deep-learning approaches (DiffDock), and includes protein-ligand interaction fingerprinting for downstream analysis.
**Pipeline Stages:**
1. **Target Preparation** -- Clean PDB structures, remove waters, add hydrogens, detect binding pockets
2. **Ligand Preparation** -- Convert SMILES to 3D, generate conformers, assign charges
3. **Docking** -- Run Vina or DiffDock to generate binding poses
4. **Scoring & Interaction Analysis** -- Identify hydrogen bonds, hydrophobic contacts, pi-stacking, salt bridges
5. **Ranking** -- Combine docking scores with interaction quality into a composite ranking
