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alphafold-database

Retrieve AlphaFold protein structures by UniProt ID and analyze pLDDT and PAE confidence metrics.

1|Updated Jan 14, 2026
Search Tags:#bioinformatics#protein structure#drug discovery#alphafold#structural biology#ai prediction
One-click install
npx skills add https://github.com/Sologa/codex-pipeline --skill alphafold-database-sologa
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: alphafold-database
Source: https://github.com/Sologa/codex-pipeline/tree/main/.codex/skills/alphafold-database
Command: npx skills add https://github.com/Sologa/codex-pipeline --skill alphafold-database-sologa

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires biopython, requests, numpy, matplotlib, pandas, scipy, google-cloud-bigquery, gsutil, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill provides access to over 200 million AI-predicted 3D protein structures, enabling researchers to analyze protein function and design new therapeutics without relying solely on experimental data.

Core Features & Use Cases

  • Structure Retrieval: Fetch protein structures by UniProt ID.
  • Confidence Analysis: Evaluate prediction reliability using pLDDT and PAE scores.
  • Bulk Data Access: Download entire proteomes or specific datasets via Google Cloud.
  • Use Case: A drug discovery team needs to investigate the structure of a novel protein target. They use this Skill to download its AlphaFold prediction, analyze its confidence metrics, and identify potential binding sites for drug candidates.

Quick Start

Use the alphafold-database skill to download the structure for UniProt ID P00520.

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 predicted protein structures by UniProt ID?▼

To download AlphaFold predicted protein structures, you query the database by providing a specific UniProt ID to programmatically retrieve the corresponding 3D protein structure files in PDB or mmCIF formats.

How can I check the reliability of an AlphaFold protein structure prediction?▼

You can check the reliability of an AlphaFold protein structure prediction by analyzing its built-in confidence metrics, specifically evaluating the pLDDT and PAE scores provided with the retrieved 3D structural data.

Can I download entire proteomes from the AlphaFold database using Google Cloud?▼

Yes, you can download entire proteomes from the AlphaFold database via Google Cloud, utilizing google-cloud-bigquery and gsutil to manage bulk data access for structural biology and drug discovery workflows.

Is there a way to retrieve 3D protein structures for novel targets without experimental data?▼

Retrieving 3D protein structures for novel targets without experimental data is possible by accessing over 200 million AI-predicted structures to analyze protein function and identify potential binding sites.

Does this AlphaFold database integration support protein engineering and drug discovery workflows?▼

Yes, this AlphaFold database integration supports protein engineering and drug discovery workflows by providing programmatic access to AI-predicted structures and confidence metrics for identifying potential binding sites.

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