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

When uncertain about any scientific fact, SEARCH databases first rather than reasoning from memory. A database-verified answer is always more reliable than a guess.