Skill v1.0.0
currentAutomated scan100/100version: "1.0.0" name: protein_structure_pipeline description: >- Protein structure obtain → confidence → visualize pipeline. Use when the user needs a 3D structure from sequence or UniProt ID, AlphaFold/ESMFold retrieval, pLDDT/PAE analysis, or structure rendering. Do NOT use for mutation ranking (zero_shot_mutation_workflow), FoldSeek search (foldseek_structural_similarity), or experimental PDB-only metadata without structure needs (rcsb_database alone may suffice). license: Apache-2.0 metadata: version: "1.0" skill-author: VenusFactory2
Protein Structure Pipeline
Overview
Chains VenusFactory structure tools: AlphaFold DB download + confidence analytics, local ESMFold when no UniProt ID, RCSB for experimental structures, and PyMOL rendering.
VenusFactory execution
Call hub tools only. Large PDB/mmCIF stay on disk via file_info.file_path.
Project Tools (VenusFactory2)
| Tool | Args | When | |
|---|---|---|---|
| download_alphafold_structure_by_uniprot_id | uniprot_id, `out_dir`, format | Known UniProt accession | |
| download_alphafold_metadata_by_uniprot_id | uniprot_id, `out_dir` | Need pLDDT metadata JSON | |
| analyze_alphafold_plddt_by_metadata_file | metadata_path | Confidence per residue | |
| analyze_alphafold_pae_by_pae_file | pae_path | Domain/interface confidence | |
| predict_structure_esmfold | sequence, optional output_dir | No UniProt / quick local fold | |
| download_rcsb_structure_by_pdb_id | pdb_id, `out_dir`, format | Experimental structure | |
| download_rcsb_entry_metadata_by_pdb_id | pdb_id, `out_path` | Resolution, method, ligands | |
| render_protein_structure | pdb_path, `out_dir`, style options | Publication-quality still | |
| superpose_two_structures | pdb_a, pdb_b, `out_dir` | Compare models |
Workflow
UniProt → AlphaFold (default)
download_alphafold_structure_by_uniprot_iddownload_alphafold_metadata_by_uniprot_id→analyze_alphafold_plddt_by_metadata_file- If PAE available,
analyze_alphafold_pae_by_pae_file - Optional
render_protein_structure(cartoon + pLDDT coloring if supported by tool args)
Sequence-only → ESMFold
- Obtain sequence (
read_fasta/ UniProt seq tool). predict_structure_esmfold- Optional RSA/SASA/SS via
protein_property_predictiontools.
Experimental PDB
download_rcsb_structure_by_pdb_id+ metadata.- Prefer over AlphaFold when an experimental entry exists for the same construct.
When NOT to use
- Structural homolog search with active-site masking →
foldseek_structural_similarity - Domain annotation without structure →
interpro_domain_annotation
Common mistakes
- Using AlphaFold when user already has a high-res PDB.
- Dumping PDB text into chat instead of using
file_info.file_path. - Skipping pLDDT before trusting loop regions for mutation design.