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alphafold-database

Retrieve AlphaFold structures and confidence metrics for UniProt accessions.

94|11|Updated Mar 26, 2026
Search Tags:#bioinformatics#pdb#pae#plddt#alphafold#protein-structure#uniprot
One-click install
npx skills add https://github.com/swaruplab/operon --skill alphafold-database-swaruplab
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: alphafold-database
Source: https://github.com/swaruplab/operon/tree/main/src-tauri/protocols/alphafold-database
Command: npx skills add https://github.com/swaruplab/operon --skill alphafold-database-swaruplab

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

Retrieves AlphaFold predictions and metadata for a given UniProt accession, enabling researchers to quickly access structure data and confidence metrics for downstream analysis.

Core Features & Use Cases

  • Structure retrieval by UniProt: Fetch AlphaFold predictions using UniProt IDs and obtain CIF/PDB files for modeling, docking, and visualization.
  • Confidence analysis: Access pLDDT and PAE metrics to assess reliability and guide interpretation of predicted structures.
  • Bulk access & integrations: Leverage Google Cloud or 3D-Beacons federated endpoints to scale analyses across proteomes or protein families.

Quick Start

Fetch the AlphaFold prediction for a UniProt ID and download the corresponding mmCIF or PDB file for immediate analysis.

Frequently Asked Questions about alphafold-database

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

FAQPage Schema
How do I fetch AlphaFold protein structures using a UniProt ID?▼

To fetch AlphaFold protein structures, provide a UniProt accession to retrieve predicted coordinates in mmCIF or PDB format along with metadata for immediate analysis.

How can I access pLDDT and PAE confidence metrics for AlphaFold predictions?▼

You can access pLDDT and PAE confidence metrics by retrieving AlphaFold predictions via UniProt accessions, allowing you to assess structure reliability and guide downstream interpretation.

Can I retrieve AlphaFold structures in bulk for proteome-scale analysis?▼

Yes, you can retrieve AlphaFold structures in bulk by leveraging Google Cloud or 3D-Beacons federated endpoints to scale analyses across protein families or entire proteomes.

Does this AlphaFold database retrieval method support Python-based pipelines?▼

Yes, this retrieval method supports programmatic access within Python-based pipelines, relying on public AlphaFold DB APIs and file endpoints for downstream workflows.

What is the best way to download mmCIF files for AlphaFold predicted structures?▼

The best way to download mmCIF files for AlphaFold predicted structures is to query the database using a UniProt identifier and fetch the corresponding coordinate files programmatically.

When should I use 3D-Beacons versus direct AlphaFold DB APIs for structure retrieval?▼

Use 3D-Beacons for federated access across multiple structure providers, while direct AlphaFold DB APIs are suited for targeted retrieval of AlphaFold-specific predictions and metadata.

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