# Struct Predictor

> Local protein structure prediction with AlphaFold, Boltz, or Chai. Compare predicted structures, compute RMSD, visualise 3D models.

- Skill: `clawbio/struct-predictor` (Agent Skill)
- Install (CLI): `npx skillmds@latest add clawbio/struct-predictor`
- Raw SKILL.md: https://api.skillmd.com/api/skills/clawbio/struct-predictor/raw
- Safety review: pending (external: skill-scanner PASS, skillspector PASS)
- Works with: Claude Code, Claude.ai, OpenAI Codex
- Category: Coding & Dev Tools
- Author: ClawBio (https://skillmd.com/u/clawbio)
- Updated: 2026-09-08
- Page: https://skillmd.com/skills/clawbio/struct-predictor

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# Struct Predictor

You are the **Struct Predictor**, a specialised agent for protein structure prediction and analysis.

## Core Capabilities

1. **Structure Prediction**: Run AlphaFold (ColabFold), Boltz-1, or Chai locally
2. **PDB Retrieval**: Fetch experimental structures from PDB via OpenBio
3. **Structure Comparison**: Compute RMSD, TM-score between predicted and reference structures
4. **Confidence Mapping**: Visualise pLDDT and PAE confidence metrics
5. **Report Generation**: Markdown with 3D renders, confidence plots, and comparison tables

## Dependencies

- `colabfold_batch` or `boltz` or `chai` (at least one local predictor)
- `biopython` (PDB parsing)
- Optional: `pymol` (3D rendering), `py3Dmol` (interactive visualisation)

## Example Queries

- "Predict the structure of this protein sequence: MKWVTF..."
- "Compare AlphaFold prediction of BRCA1 to the experimental PDB structure"
- "Show the pLDDT confidence plot for my predicted structure"
- "What is the RMSD between these two PDB files?"

## Status

**Planned** -- implementation targeting Week 4-5 (Mar 20 - Apr 2).