AD
Data & Repro
Adaptyv
Adaptyv is a cloud laboratory platform that provides automated protein testing and validation services. Submit protein sequences via API or…
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Data & Repro
TO
tooluniverse-protein-structure-retrieval
Maintainer FreedomIntelligence · Last updated April 1, 2026
Retrieves protein structure data from RCSB PDB, PDBe, and AlphaFold with protein disambiguation, quality assessment, and comprehensive structural profiles. Creates detailed structure reports with experimental metadata, ligand information, and download links. Use when users need protein structures, 3D models, crystallography data, or mention PDB IDs (4-character codes like 1ABC) or UniProt accessions.
Original source
FreedomIntelligence/OpenClaw-Medical-Skills
https://github.com/FreedomIntelligence/OpenClaw-Medical-Skills/tree/main/skills/tooluniverse-protein-structure-retrieval
- Maintainer
- FreedomIntelligence
- License
- MIT
- Last updated
- April 1, 2026
Skill Snapshot
Key Details From SKILL.md
Key Notes
- Retrieve protein structures with proper disambiguation, quality assessment, and comprehensive metadata.
- IMPORTANT: Always use English terms in tool calls (protein names, organism names), even if the user writes in another language. Only try original-language terms as a fallback if English returns no results. Respond in the user's language.
- if user_provided_pdb_id: # Direct structure retrieval pdb_id = user_provided_pdb_id.upper() elif user_provided_uniprot: # Get UniProt info, then search structures uniprot_id = user_provided_uniprot # Can also get AlphaFold structure af_structure = tu.tools.alphafold_get_structure_by_uniprot( uniprot_id=uniprot_id ) elif user_provided_protein_name: # Search by name result = tu.tools.search_structures_by_protein_name( protein_name=protein_name ).
Source Doc
Excerpt From SKILL.md
Phase 0: Clarification (When Needed)
Ask the user ONLY if:
- Protein name matches multiple genes/families (e.g., "kinase" → which kinase?)
- Organism not specified for conserved proteins
- Intent unclear: need experimental structure vs AlphaFold prediction?
Skip clarification for:
- Specific PDB IDs (4-character codes)
- UniProt accessions
- Unambiguous protein names with organism
1.1 Resolve Protein Identity
from tooluniverse import ToolUniverse
tu = ToolUniverse()
tu.load_tools()
## 1.2 Identity Resolution Checklist
- [ ] Protein name/gene identified
- [ ] Organism confirmed
- [ ] UniProt accession (if available)
- [ ] Isoform/variant specified (if relevant)
Use cases
- Use when users need protein structures, 3D models, crystallography data, or mention PDB IDs (4-character codes like 1ABC) or UniProt accessions.
Not for
- Do not rely on this catalog entry alone for installation or maintenance details.
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