protein-structure-pipeline

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)

1. download_alphafold_structure_by_uniprot_id
2. download_alphafold_metadata_by_uniprot_id → analyze_alphafold_plddt_by_metadata_file
3. If PAE available, analyze_alphafold_pae_by_pae_file
4. Optional render_protein_structure (cartoon + pLDDT coloring if supported by tool args)

Sequence-only → ESMFold

1. Obtain sequence (read_fasta / UniProt seq tool).
2. predict_structure_esmfold
3. Optional RSA/SASA/SS via protein_property_prediction tools.

Experimental PDB

1. download_rcsb_structure_by_pdb_id + metadata.
2. 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.