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alphafold-database

Retrieve AlphaFold protein structures by UniProt ID and download mmCIF or PDB files.

1|Updated Mar 4, 2026
Search Tags:#pdb#pae#plddt#alphafold#uniprot#protein-structures#mmcif
One-click install
npx skills add https://github.com/Hung-3008/agusta --skill alphafold-database-hung-3008
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: alphafold-database
Source: https://github.com/Hung-3008/agusta/tree/main/.agents/skills/alphafold-database
Command: npx skills add https://github.com/Hung-3008/agusta --skill alphafold-database-hung-3008

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

AlphaFold DB provides easy access to AI-predicted protein structures, enabling retrieval by UniProt ID, downloading coordinate files (mmCIF/PDB), and analyzing confidence metrics (pLDDT, PAE) to accelerate structure-guided research.

Core Features & Use Cases

  • Retrieve predictions by UniProt accession (e.g., AF- entries) and protein name.
  • Download model coordinates (mmCIF/PDB) and confidence data (pLDDT, PAE) for downstream analysis.
  • Access bulk datasets via Google Cloud and integrate predictions into computational pipelines for drug discovery, protein engineering, and evolutionary studies.

Quick Start

Use this skill to fetch a structure by UniProt ID and download the corresponding model file to your workspace.

Frequently Asked Questions about alphafold-database

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

FAQPage Schema
How do I download AlphaFold protein structures by UniProt ID?▼

AlphaFold confidence metrics like pLDDT and PAE are accessed by querying specific UniProt accessions through the AlphaFold API, which returns the prediction data alongside the mmCIF or PDB model files for analysis.

Can I retrieve AlphaFold model coordinates in mmCIF and PDB formats?▼

Yes, you can retrieve AlphaFold model coordinates in both mmCIF and PDB formats by querying the AlphaFold API with a UniProt ID and downloading the associated structure files for downstream analysis.

How do I get AlphaFold pLDDT and PAE confidence data for downstream analysis?▼

AlphaFold confidence metrics like pLDDT and PAE are accessed by querying specific UniProt accessions through the AlphaFold API, which returns the prediction data alongside the mmCIF or PDB model files for analysis.

Does this approach support bulk AlphaFold dataset workflows via Google Cloud?▼

Yes, this approach supports bulk AlphaFold dataset workflows by enabling programmatic access to bulk Google Cloud datasets, allowing large-scale integration of predictions into computational pipelines.

What's the best way to integrate AlphaFold predictions into drug discovery pipelines?▼

The best way to integrate AlphaFold predictions into drug discovery pipelines is to programmatically query the AlphaFold API by UniProt ID, downloading the coordinate and confidence data directly into your analysis workflows.

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