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pdb-database

Search RCSB Protein Data Bank and download structure files via API.

269|20|Updated Jun 13, 2026
Search Tags:#bioinformatics#data retrieval#pdb#protein#structural biology#biomolecules
One-click install
npx skills add https://github.com/NeuroAIHub/BrainPilot --skill pdb-database-neuroaihub
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: pdb-database
Source: https://github.com/NeuroAIHub/BrainPilot/tree/main/packages/skills/skills/09_Cellular_Molecular_Neuroscience/pdb-database
Command: npx skills add https://github.com/NeuroAIHub/BrainPilot --skill pdb-database-neuroaihub

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires polite-http, and includes scripts (resource) components.

What problem does it solve?

This skill streamlines the complex process of searching, filtering, and downloading high-quality 3D biomolecular structure data from the RCSB Protein Data Bank, removing the need for manual web browsing and manual file handling.

Core Features & Use Cases

  • Advanced Search: Perform sequence, structure, chemical, and full-text searches to find specific proteins or ligands.
  • Metadata Retrieval: Efficiently fetch specific experimental metadata or taxonomy information using GraphQL queries.
  • Automated Downloads: Batch download coordinate files in mmCIF or PDB formats for downstream analysis.
  • Use Case: A researcher needs to identify all non-human protein structures containing a specific calcium ion binding site and download their coordinate files for molecular dynamics simulations.

Quick Start

Use the pdb-database skill to search for all structures containing the chemical component CA and download the results.

Frequently Asked Questions about pdb-database

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

FAQPage Schema
How do I batch download 3D biomolecular structures from the RCSB Protein Data Bank?▼

You can batch download 3D biomolecular structures from the RCSB Protein Data Bank using automated workflows that retrieve coordinate files in mmCIF or PDB formats for downstream analysis.

Can I search for protein structures by sequence similarity and chemical attributes?▼

Yes, you can search for protein structures by performing sequence similarity, chemical attribute, and metadata-based discovery to identify specific proteins or ligands.

How do I retrieve experimental metadata for biomolecules using GraphQL?▼

You can retrieve experimental metadata or taxonomy information for biomolecules by executing GraphQL queries to extract specific data from the RCSB Protein Data Bank.

Does this approach handle rate limiting when retrieving structural biology data?▼

Yes, rate-limited automated workflows are implemented to manage data retrieval and coordinate file downloads, ensuring stable access to structural biology data.

What is the best way to find protein structures with specific ligands without manual web browsing?▼

The best way to find protein structures with specific ligands is using structured API queries that perform advanced chemical and full-text searches, removing the need for manual web browsing.

Can I use structured API queries to find non-human protein structures with specific ion binding sites?▼

Yes, you can use structured API queries to filter structures by taxonomy and chemical components, identifying non-human protein structures containing specific calcium ion binding sites.

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