---
name: autodock-docking-engine
description: AutoDock molecular docking skill for small molecule binding prediction and virtual screening
allowed-tools:
  - Read
  - Write
  - Glob
  - Grep
  - Edit
  - WebFetch
  - WebSearch
  - Bash
metadata:
  version: "1.0"
  category: bioinformatics
  tags:
    - structural-biology
    - docking
    - virtual-screening
    - drug-discovery
---

# 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)