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query-alphafold

Query the AlphaFold EBI API for UniProt protein structures and retrieve PDB/CIF files and confidence metrics.

401|53|Updated Feb 26, 2026
Search Tags:#pdb#structure-download#pae#plddt#alphafold#protein-structure#uniprot
One-click install
npx skills add https://github.com/Runchuan-BU/BioClaw --skill query-alphafold
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: query-alphafold
Source: https://github.com/Runchuan-BU/BioClaw/tree/main/.claude/skills/query-alphafold
Command: npx skills add https://github.com/Runchuan-BU/BioClaw --skill query-alphafold

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Enable researchers to quickly obtain predicted 3D protein models, confidence metrics, and downloadable structure files from the AlphaFold EBI service without manual API exploration or file retrieval.

Core Features & Use Cases

  • Query AlphaFold prediction metadata for a UniProt accession and retrieve model summaries including organism, gene, and global confidence metrics.
  • Download structure files in PDB or CIF format and obtain visualization resources such as PAE and pLDDT references for downstream rendering or analysis.
  • Use Case: Given a UniProt ID for a protein of interest, automatically fetch the predicted model, grab its PAE/plddt images, and save the PDB/CIF to a shared workspace for visualization or comparison with experimental structures.

Quick Start

Query AlphaFold for UniProt P04637 and download the PDB and pLDDT summary to the workspace.

Frequently Asked Questions about query-alphafold

High-intent search queries and answers about installing and using this skill.

FAQPage Schema
How do I download AlphaFold predicted protein structures using a UniProt accession ID?▼

AlphaFold confidence metrics like pLDDT and PAE are obtained by querying the AlphaFold EBI API with a UniProt ID. The Skill retrieves per-residue pLDDT scores and PAE image URLs for downstream visualization.

Can I retrieve AlphaFold PAE and pLDDT confidence metrics for downstream visualization?▼

AlphaFold confidence metrics like pLDDT and PAE are obtained by querying the AlphaFold EBI API with a UniProt ID. The Skill retrieves per-residue pLDDT scores and PAE image URLs for downstream visualization.

What is needed to fetch AlphaFold 3D models and metadata programmatically?▼

AlphaFold structure files are available in both PDB and CIF formats for download. The Skill queries the AlphaFold EBI service and retrieves either format to support various molecular visualization and comparison tools.

Does this tool work with both PDB and CIF format files for protein structure download?▼

AlphaFold structure files are available in both PDB and CIF formats for download. The Skill queries the AlphaFold EBI service and retrieves either format to support various molecular visualization and comparison tools.

When should I use AlphaFold predictions instead of experimental protein structures?▼

AlphaFold predictions are suitable when experimental structures are unavailable and you need a predicted 3D model. The Skill provides global confidence metrics to help evaluate model reliability for comparison with experimental data.

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