alphafold-database

name	alphafold_database
description	AlphaFold DB structures and confidence analytics via VenusFactory tools. Use when the user needs predicted structures by UniProt ID, pLDDT/PAE analysis, or PDB/mmCIF download. Do NOT use for experimental PDB (rcsb_database), local ESMFold without UniProt (predict_structure_esmfold / protein_structure_pipeline), or sequence annotation (uniprot_database).
license	Unknown
metadata	{"version":"1.2","skill-author":"VenusFactory2"}

AlphaFold Database

Overview

Download AlphaFold predictions to disk and analyze confidence locally. Default model version is v6. Large coordinate files must stay on disk — never paste PDB into chat.

VenusFactory execution

Call hub tools by exact name. Extended Biopython/GCP examples: read_skill(..., relative_path="references/legacy_guide.md") or references/api_reference.md.

Project Tools (VenusFactory2)

Tool	Args	Returns	Description
download_alphafold_structure_by_uniprot_id	uniprot_id, out_dir, format (pdb|cif, default pdb), version (default v6), fragment	rich JSON status + file_info	Structure file
download_alphafold_metadata_by_uniprot_id	uniprot_id, out_dir	rich JSON + metadata JSON path	Prediction metadata
analyze_alphafold_plddt_by_metadata_file	metadata_path	pLDDT fractions + verdict	Local analysis
analyze_alphafold_pae_by_pae_file	pae_path, optional cutoffs	domains + PAE stats	Local analysis

There is no dedicated PAE download @tool. Obtain PAE via metadata paeDocUrl + agent_generated_code, then analyze.

Recommended workflow

1. download_alphafold_metadata_by_uniprot_id → analyze_alphafold_plddt_by_metadata_file
2. download_alphafold_structure_by_uniprot_id for coordinates
3. Optional PAE download → analyze_alphafold_pae_by_pae_file
4. Optional render_protein_structure / figure step for pLDDT plot

When NOT to use

• Experimental structure → rcsb_database
• No UniProt, only raw sequence → predict_structure_esmfold
• Full engineering pipeline → protein_structure_pipeline

Common mistakes

• Assuming return shape is {success, file_path} — use status + file_info.file_path
• Using v4 URLs while tools default to v6
• Feeding structure PDB into the pLDDT analyzer (needs metadata JSON)
• Dumping coordinates into the conversation

References

• references/api_reference.md — REST/URL details
• references/legacy_guide.md — archived tutorials (Biopython, GCP bulk)