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alterlab-alphafold-db

Retrieve AlphaFold predictions and model files by UniProt accession.

58|9|Updated Mar 16, 2026
Search Tags:#bioinformatics#pae#plddt#alphafold#protein-structure#uniprot
One-click install
npx skills add https://github.com/AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-alphafold-db
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: alterlab-alphafold-db
Source: https://github.com/AlterLab-IEU/AlterLab-Academic-Skills/tree/main/skills/databases/alterlab-alphafold-db
Command: npx skills add https://github.com/AlterLab-IEU/AlterLab-Academic-Skills --skill alterlab-alphafold-db

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

AlphaFold DB access and integration for retrieving structure predictions, confidence metrics, and files programmatically.

Core Features & Use Cases

  • Retrieve AlphaFold predictions by UniProt; download model files (mmCIF/BCIF/PDB) and access confidence metrics (pLDDT, PAE); filter by taxonomy; bulk-download via Google Cloud; integrate with downstream analysis.
  • Compare and extract data for structural biology workflows, drug discovery, and proteome-wide analyses.
  • Use Case: Imagine you need AF models for a list of UniProt accessions and want to batch download all corresponding model files and confidence data for analysis.

Quick Start

Execute a script that fetches the AlphaFold prediction for a UniProt accession and downloads its model file and confidence JSON.

Frequently Asked Questions about alterlab-alphafold-db

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

FAQPage Schema
How do I download AlphaFold protein structures for a specific UniProt accession?▼

You can download AlphaFold protein structures by querying with a UniProt accession to retrieve direct download links for model files in mmCIF, BCIF, or PDB formats.

Can I batch download AlphaFold model files and confidence data for multiple proteins?▼

Yes, you can batch download AlphaFold model files and confidence metrics by utilizing the bulk data access available through Google Cloud integration.

How do I retrieve per-residue confidence scores like pLDDT and PAE from AlphaFold predictions?▼

You retrieve per-residue confidence scores by accessing the pLDDT and PAE metrics associated with a given AlphaFold prediction entry for structural analysis.

Does this approach expose AlphaFold entry metadata such as version history for reproducible research?▼

Yes, this approach exposes AlphaFold entry metadata including entryId, cifUrl, and version history to ensure your structural biology workflows remain reproducible.

What is the best way to integrate AlphaFold DB predictions into downstream structural biology workflows?▼

The best way to integrate AlphaFold DB predictions is to programmatically fetch model files and confidence JSON data for downstream drug discovery and proteome-wide analysis.

Can I filter AlphaFold structure predictions by taxonomy?▼

Yes, you can filter AlphaFold structure predictions by taxonomy to narrow down proteome-wide analyses to specific organisms of interest.

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