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alphafold_database

Retrieve AlphaFold predictions and metadata by UniProt ID.

249|35|Updated May 8, 2024
Search Tags:#structure-download#pae#alphafold#bulk-download#protein-structure#uniprot#confidence-metrics
One-click install
npx skills add https://github.com/ai4protein/VenusFactory --skill alphafold-database-ai4protein
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: alphafold_database
Source: https://github.com/ai4protein/VenusFactory/tree/main/src/agent/skills/alphafold_database
Command: npx skills add https://github.com/ai4protein/VenusFactory --skill alphafold-database-ai4protein

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

AlphaFold predictions and metadata are scattered across multiple access points. This Skill provides unified programmatic access to search by UniProt ID, retrieve structure files (cif/pdb), and download confidence metrics and PAE data for downstream analyses.

Core Features & Use Cases

  • Retrieve AlphaFold predictions by UniProt ID and download model files (cif/bcif/pdb) for local analysis.
  • Access confidence metrics (pLDDT) and Predicted Aligned Error (PAE) data to evaluate reliability.
  • Use bulk data access via Google Cloud and BigQuery for large-scale studies and reproducible pipelines.

Quick Start

Query AlphaFold predictions by UniProt ID and download model, confidence, and PAE data for your analysis.

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?▼

You can download AlphaFold protein structures by querying a UniProt ID to retrieve model files in cif, bcif, or pdb format for local structural biology analysis.

What are pLDDT and PAE confidence metrics in AlphaFold predictions?▼

pLDDT and PAE are confidence metrics evaluating AlphaFold prediction reliability. pLDDT measures local structure confidence, while Predicted Aligned Error estimates domain positioning accuracy.

Can I bulk download AlphaFold data via Google Cloud and BigQuery?▼

Yes, bulk AlphaFold data access is supported via Google Cloud and BigQuery, enabling large-scale protein structure studies and reproducible automated analysis pipelines.

What is the default AlphaFold database version used for structure retrieval?▼

The default AlphaFold database version applied for protein structure retrieval is v4, ensuring consistent access to predicted models, confidence scores, and PAE data.

How do I programmatically access AlphaFold metadata for automated workflows?▼

Programmatic AlphaFold access integrates with agent tools wrapping query and download functions, retrieving structure files, pLDDT scores, and PAE data by UniProt ID for automated workflows.

What file formats are available for AlphaFold protein structure download?▼

Available AlphaFold protein structure download formats include cif, bcif, and pdb files, retrievable by UniProt ID for downstream structural biology analysis.

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