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pdb-database

Search and retrieve 3D macromolecular structures from the RCSB Protein Data Bank.

1.1k|99|Updated Feb 12, 2026
Search Tags:#bioinformatics#protein structure#drug discovery#pdb#rcsb#structural biology
One-click install
npx skills add https://github.com/dp-archive/archive --skill pdb-database-dp-archive
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: pdb-database
Source: https://github.com/dp-archive/archive/tree/main/seed_skills/pdb-database
Command: npx skills add https://github.com/dp-archive/archive --skill pdb-database-dp-archive

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill provides access to the RCSB PDB, enabling users to find, download, and analyze 3D protein and nucleic acid structures, streamlining research in structural biology and drug discovery.

Core Features & Use Cases

  • Structure Searching: Find structures by text, sequence, or structural similarity.
  • Data Retrieval: Download coordinate files (PDB, mmCIF) and retrieve metadata.
  • Use Case: A researcher needs to find all human hemoglobin structures resolved below 2.0 Å resolution to study oxygen binding. This Skill can perform that search and provide the relevant PDB IDs and download links.

Quick Start

Search for all human protein structures with a resolution less than 2.0 Angstroms.

Frequently Asked Questions about pdb-database

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

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

To search protein structures in the RCSB PDB, you can query by text, sequence, or structural similarity. This allows you to find specific macromolecular structures, such as human proteins resolved below 2.0 Angstroms, and retrieve their PDB IDs.

Can I download mmCIF and PDB coordinate files programmatically?▼

Yes, you can download coordinate files in both PDB and mmCIF formats. The Skill provides programmatic access to retrieve 3D macromolecular structures and associated metadata directly from the RCSB database for structural biology research.

What is the best way to perform batch operations for drug discovery structure retrieval?▼

The best way to retrieve structures for drug discovery is using batch operations through the rcsb-api. This facilitates searching by text or sequence similarity and downloading multiple coordinate files to streamline your research workflow.

Does this Skill require the rcsb-api package to search structural biology data?▼

Yes, the Skill requires the rcsb-api dependency to interact with PDB data. It leverages this Python package to provide seamless access to search functionalities and retrieve 3D macromolecular structures and metadata.

How do I find all human hemoglobin structures to study oxygen binding?▼

You can find human hemoglobin structures by executing a text search for the specific organism and resolution. The Skill will query the RCSB PDB and return the relevant PDB IDs and download links for your structural analysis.

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