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query-alphafold

Query AlphaFold EBI API for protein structure predictions and download PDB or CIF files.

30|2|Updated Mar 13, 2026
Search Tags:#bioinformatics#download#pdb#alphafold#protein-structure#uniprot#structure-prediction
One-click install
npx skills add https://github.com/IDEA-XL/MolClaw --skill query-alphafold-idea-xl
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: query-alphafold
Source: https://github.com/IDEA-XL/MolClaw/tree/main/.claude/skills/query-alphafold
Command: npx skills add https://github.com/IDEA-XL/MolClaw --skill query-alphafold-idea-xl

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Query AlphaFold protein structure predictions via the AlphaFold EBI API for specified UniProt IDs to streamline structure discovery and data retrieval.

Core Features & Use Cases

  • Retrieve prediction metadata from the AlphaFold API for a given protein.
  • Download predicted structures in PDB or CIF formats.
  • Retrieve per-residue confidence (pLDDT) and related metrics for structural interpretation.
  • Use case: A researcher wants to compare predicted structure of TP53 to literature models and automatically fetch PDB files for visualization.

Quick Start

Ask me for the AlphaFold prediction of a UniProt ID to fetch model info and download the corresponding structure file.

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 protein structure predictions using a UniProt ID?▼

You can download AlphaFold protein structure predictions by querying the AlphaFold EBI API with a specific UniProt ID to retrieve and download model files in PDB or CIF formats.

Can I retrieve per-residue confidence metrics for an AlphaFold predicted structure?▼

Yes, querying the AlphaFold EBI API for a UniProt ID retrieves per-residue confidence data, such as pLDDT scores, required for structural interpretation of the predicted protein structure.

What is the best way to get AlphaFold model info and PDB files for visualization?▼

The best way to get AlphaFold model info and PDB files for visualization is to request the AlphaFold prediction for a UniProt ID, which fetches metadata and downloads the corresponding structure file.

Do I need to provide a UniProt ID to fetch AlphaFold structure data?▼

Yes, you must provide a valid UniProt ID because the AlphaFold EBI API requires this specific identifier to fetch prediction metadata, confidence scores, and downloadable structure files.

Does this method support downloading structures in both PDB and CIF formats?▼

Yes, fetching AlphaFold structure predictions via the EBI API supports downloading the predicted 3D structures in both PDB and CIF formats for subsequent analysis and visualization.

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