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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 graph: domains: [domain:bioinformatics] specializations: [specialization:biomedical-informatics] skillAreas: [skill-area:physics-simulation, skill-area:statistical-analysis, skill-area:data-analysis] workflows: [workflow:experiment-design] roles: [role:research-scientist, role:biomedical-engineer]

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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)