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pocket-detection

Multi-method binding pocket detection and druggability assessment. Grid-based, fpocket, and P2Rank detection with druggability scoring, visualization, and cross-structure comparison.

backend/cli/skills/chemistry/pocket-detection/SKILL.md

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# Pocket Detection & Druggability Assessment

## Overview

This skill provides multi-method binding pocket detection on protein structures, druggability scoring, pocket visualization, and cross-structure pocket comparison. It is the first dedicated step in any structure-based drug design workflow — identifying **where** on a protein a small molecule can bind before docking or de novo design begins.

**Key capabilities:**
- **Three detection methods**: grid-based cavity scan, fpocket (alpha spheres), P2Rank (machine learning)
- **Druggability scoring**: 6-axis weighted assessment (volume, hydrophobicity, enclosure, depth, H-bond capacity, aromaticity)
- **Visualization**: summary panels, residue composition, druggability radar, method comparison plots
- **Cross-structure comparison**: match pockets across apo/holo, wild-type/mutant, or predicted/experimental structures

## When to Use This Skill