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pdb-database

Search RCSB PDB by text, sequence, or structure and download coordinates and metadata.

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

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires rcsb-api, requests, biopython, and includes scripts (resource) and references (resource) components.

What problem does it solve?

This Skill provides access to the RCSB PDB, enabling users to find and retrieve 3D structural data for proteins and nucleic acids, which is crucial for research and discovery.

Core Features & Use Cases

  • Structure Search: Find PDB entries using text, sequence, or structural similarity.
  • Data Retrieval: Download coordinate files (PDB, mmCIF) and retrieve metadata.
  • Use Case: A researcher needs to find all human protein structures with a resolution better than 2.0 Å to study a specific disease pathway.

Quick Start

Use the pdb-database skill to search for human protein structures with a resolution less than 2.0.

Frequently Asked Questions about pdb-database

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

FAQPage Schema
How do I search for protein structures in the PDB database by resolution and organism?▼

To search for protein structures in the PDB database, use text-based queries to filter entries by specific criteria like organism and resolution threshold, retrieving matching structural data and metadata.

Can I download mmCIF and PDB coordinate files programmatically for drug discovery?▼

Yes, you can download coordinate files including mmCIF and PDB formats programmatically, retrieving 3D structural data and metadata essential for structural biology and drug discovery workflows.

What is the best way to find 3D protein structures using sequence similarity?▼

Finding 3D protein structures via sequence similarity involves querying the repository with an input sequence to locate and retrieve matching experimentally determined structural entries.

Does this PDB data retrieval method support nucleic acid structures as well as proteins?▼

Yes, this PDB data retrieval method supports accessing 3D structures for both proteins and nucleic acids, enabling comprehensive structural biology research and data extraction.

How do I retrieve metadata for PDB entries using biopython and the rcsb-api?▼

Retrieve PDB entry metadata by leveraging programmatic access through the rcsb-api and biopython dependencies, extracting comprehensive annotation data alongside the 3D coordinate files.

Are there limitations to searching the RCSB PDB for structural biology workflows?▼

Limitations of searching the RCSB PDB include relying solely on experimentally determined structures, meaning predicted models are excluded from the structural biology data retrieval results.

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