Individual skill
tooluniverse-protein-structure-prediction
Protein 3D structure prediction from sequence — ESMFold de novo prediction, AlphaFold database retrieval, experimental structures from RCSB, ProtVar variant impact assessment, ProtParam sequence properties. Use for structure prediction when no experimental structure exists, fold-confidence scoring, and structure-guided variant interpretation.
plugin/skills/tooluniverse-protein-structure-prediction/SKILL.md
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# Protein Structure Prediction and Analysis
End-to-end workflow for protein structure prediction starting from a sequence or UniProt accession. Combines ESMFold de novo prediction, AlphaFold database retrieval, experimental structure benchmarking from RCSB, ProtVar variant impact assessment, and ProtParam sequence property calculation.
**KEY PRINCIPLES**:
1. **Sequence first** — obtain or verify the protein sequence before prediction
2. **ESMFold for fast de novo** — works directly on sequence (up to ~800 residues); no database lookup needed
3. **AlphaFold for reference** — retrieve precomputed AlphaFold model for comparison; use `qualifier` parameter (UniProt accession)
4. **Quality before interpretation** — always report pLDDT scores; do not interpret low-confidence regions as folded
5. **Experimental validation** — compare predictions to RCSB experimental structures when available
6. **ProtVar for variants** — use when the question involves mutations or SNVs affecting structure
7. **English-first queries** — use English protein names in all tool calls; respond in the user's language
## LOOK UP, DON'T GUESS