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query-alphafold

Query the AlphaFold EBI API for protein structures and pLDDT scores by UniProt ID.

1|Updated Mar 12, 2026
Search Tags:#bioinformatics#protein structure#prediction#alphafold#uniprot#structural biology
One-click install
npx skills add https://github.com/yf8578/clawomics --skill query-alphafold-yf8578
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: query-alphafold
Source: https://github.com/yf8578/clawomics/tree/main/skills/query-alphafold
Command: npx skills add https://github.com/yf8578/clawomics --skill query-alphafold-yf8578

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires requests, json, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill retrieves predicted 3D protein structures and associated confidence metrics from the AlphaFold database, simplifying structural biology analysis.

Core Features & Use Cases

  • Structure Prediction Retrieval: Access predicted protein structures for any given UniProt ID.
  • Confidence Assessment: Obtain per-residue confidence scores (pLDDT) and overall model quality.
  • File Downloading: Download structure files in PDB or CIF formats.
  • Use Case: A researcher needs to understand the predicted 3D shape of a newly identified protein to hypothesize its function. They use this Skill with the protein's UniProt ID to get the structure file and confidence scores.

Quick Start

Use the query-alphafold skill to get the prediction information for UniProt ID P04637.

Frequently Asked Questions about query-alphafold

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

FAQPage Schema
How do I retrieve AlphaFold protein structure predictions using a UniProt ID?▼

To retrieve AlphaFold protein structure predictions, provide a specific UniProt ID to query the AlphaFold EBI API and obtain predicted 3D coordinates, per-residue confidence scores, and download links. This fetches model information directly from the database.

Can I download AlphaFold predicted structures in PDB or CIF formats?▼

Yes, you can download AlphaFold predicted structures in both PDB and CIF formats. The Skill queries the EBI API to retrieve direct download links for the structure files associated with your specified UniProt ID.

How do I get per-residue confidence scores (pLDDT) for an AlphaFold model?▼

You can get per-residue confidence scores (pLDDT) by querying the AlphaFold EBI API with a UniProt ID. The Skill fetches these confidence metrics alongside the overall model quality to help assess the reliability of the predicted structure.

What is the best way to fetch AlphaFold model information for structural bioinformatics workflows?▼

The best way to fetch AlphaFold model information for structural bioinformatics is to query the EBI API with the target UniProt ID. This retrieves the predicted 3D shape and associated metrics needed to hypothesize protein function.

Do I need a specific UniProt ID to access AlphaFold data?▼

Yes, you need a specific UniProt ID to access AlphaFold data. The retrieval process requires this unique identifier to query the EBI API and fetch the corresponding protein structure predictions and confidence scores.

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