Alphafold Predictor

---
name: alphafold-predictor
description: AlphaFold protein structure prediction skill with confidence assessment and model analysis
allowed-tools:
  - Read
  - Write
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  - WebFetch
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metadata:
  version: "1.0"
  category: bioinformatics
  tags:
    - structural-biology
    - structure-prediction
    - alphafold
    - protein
graph:
  domains: [domain:bioinformatics]
  specializations: [specialization:biomedical-informatics]
  skillAreas: [skill-area:machine-learning-frameworks, skill-area:python-data-pipelines, skill-area:data-analysis]
  workflows: [workflow:experiment-design]
  roles: [role:research-scientist, role:biomedical-engineer]
---

# AlphaFold Predictor Skill

## Purpose
Enable AlphaFold protein structure prediction with confidence assessment and model analysis.

## Capabilities
- Structure prediction execution
- pLDDT confidence scoring
- PAE analysis
- Multi-chain complex prediction
- Template-based refinement
- ColabFold integration

## Usage Guidelines
- Review pLDDT scores for prediction confidence
- Analyze PAE for domain boundaries
- Predict complexes for multi-protein assemblies
- Use templates when homologs exist
- Validate predictions against experimental data
- Document model versions and parameters

## Dependencies
- AlphaFold2
- ColabFold
- RoseTTAFold

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