# Autodock Docking Engine

> AutoDock molecular docking skill for small molecule binding prediction and virtual screening

- Skill: `a5c-ai/autodock-docking-engine` (Agent Skill)
- Install (CLI): `npx skillmds@latest add a5c-ai/autodock-docking-engine`
- Raw SKILL.md: https://api.skillmd.com/api/skills/a5c-ai/autodock-docking-engine/raw
- Safety review: pending (external: skill-scanner PASS, skillspector PASS)
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: a5c-ai (https://skillmd.com/u/a5c-ai)
- Updated: 2026-09-09
- Page: https://skillmd.com/skills/a5c-ai/autodock-docking-engine

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# AutoDock Docking Engine Skill

## Purpose
Provide AutoDock molecular docking for small molecule binding prediction and virtual screening.

## Capabilities
- Receptor and ligand preparation
- Grid generation and docking
- Scoring function evaluation
- Pose clustering and ranking
- Batch virtual screening
- Binding affinity prediction

## Usage Guidelines
- Prepare receptor and ligand structures properly
- Define appropriate grid box dimensions
- Validate docking protocol with known binders
- Cluster poses by binding mode
- Screen compound libraries efficiently
- Document docking parameters

## Dependencies
- AutoDock Vina
- GOLD
- Glide
- rDock

## Process Integration
- Molecular Docking and Virtual Screening (molecular-docking)
- Protein Structure Prediction (protein-structure-prediction)