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alphafold-database

Fetch AlphaFold DB predictions and confidence scores by UniProt ID.

75|7|Updated Feb 14, 2026
Search Tags:#bioinformatics#pdb#pae#plddt#alphafold#uniprot#protein-structures
One-click install
npx skills add https://github.com/jiaxiaojunQAQ/SkillJect --skill alphafold-database-jiaxiaojunqaq
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: alphafold-database
Source: https://github.com/jiaxiaojunQAQ/SkillJect/tree/main/data/skills_sample/alphafold-database
Command: npx skills add https://github.com/jiaxiaojunQAQ/SkillJect --skill alphafold-database-jiaxiaojunqaq

SYSTEM DOCUMENTATION & REQUIREMENTS

What problem does it solve?

Retrieve and integrate AlphaFold's 3D protein structures and confidence data for research and development workflows, eliminating manual lookup steps.

Core Features & Use Cases

  • Retrieve predictions by UniProt ID and access metadata such as entryId, gene, organism, and version history.
  • Download structure files in mmCIF, BCIF, or PDB formats and analyze confidence metrics (pLDDT and PAE) for reliability.
  • Access bulk data and workflow integrations via Google Cloud, REST endpoints, and BigQuery metadata to support scalable analyses.

Quick Start

Query AlphaFold predictions by UniProt ID via the API to fetch the latest model metadata and download URLs.

Frequently Asked Questions about alphafold-database

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

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

You can fetch AlphaFold protein structures by querying the AlphaFold DB API with a UniProt ID. This retrieves the latest model metadata, entry details, and versioned download URLs for your structural biology workflows.

What AlphaFold confidence metrics can I retrieve to evaluate protein structure reliability?▼

You can retrieve per-residue pLDDT and PAE metrics. These confidence scores indicate the reliability of specific regions within the predicted 3D protein models for drug discovery applications.

Can I download AlphaFold prediction files in PDB and mmCIF formats?▼

Yes, you can download AlphaFold prediction files in PDB, mmCIF, and BCIF formats. The API provides versioned file URLs to ensure you access the exact structural model version required for protein engineering.

Does this AlphaFold database integration support batch processing and BigQuery metadata?▼

Yes, batch processing is supported alongside access to bulk data via Google Cloud, REST endpoints, and BigQuery metadata. This enables scalable analyses and workflow integrations for large protein datasets.

What is the best way to access AlphaFold DB predictions for drug discovery workflows?▼

The best way to access AlphaFold DB predictions for drug discovery is using programmatic API queries by UniProt ID. This eliminates manual lookup steps and directly integrates model files and confidence metrics into your analysis pipelines.

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