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pdb-database

Search and retrieve 3D macromolecular structures from the RCSB PDB.

557|98|Updated Nov 7, 2025
Search Tags:#bioinformatics#protein structure#drug discovery#data retrieval#pdb#structural biology
One-click install
npx skills add https://github.com/jimmc414/Kosmos --skill pdb-database-jimmc414
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: pdb-database
Source: https://github.com/jimmc414/Kosmos/tree/main/kosmos-claude-scientific-skills/scientific-skills/pdb-database
Command: npx skills add https://github.com/jimmc414/Kosmos --skill pdb-database-jimmc414

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 programmatic access to the RCSB Protein Data Bank, enabling users to search for, retrieve, and analyze 3D structural data of biological macromolecules, streamlining research in structural biology and drug discovery.

Core Features & Use Cases

  • Structure Searching: Find protein and nucleic acid structures using text, sequence, or structural similarity.
  • Data Retrieval: Download coordinate files (PDB, mmCIF) and retrieve detailed metadata.
  • Use Case: A researcher needs to find all human protein structures determined by X-ray crystallography with a resolution better than 2.0 Å to study a specific protein family.

Quick Start

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

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 RCSB PDB using Python?▼

You can search the RCSB PDB for protein structures programmatically using Python by applying text, sequence, or structural similarity queries to retrieve matching 3D macromolecular data.

Can I retrieve mmCIF and PDB coordinate files for biological macromolecules?▼

Yes, you can retrieve and download 3D structural data of biological macromolecules directly from the RCSB PDB in various data retrieval formats, including PDB and mmCIF coordinate files.

What is the best way to find human protein structures determined by X-ray crystallography with a specific resolution?▼

Finding human protein structures determined by X-ray crystallography with a resolution better than 2.0 Å is achieved by using specific text search queries against the RCSB PDB database.

Does this RCSB API integration support sequence similarity searching for drug discovery?▼

Yes, the RCSB API integration supports sequence similarity searching alongside text and structure similarity searches to facilitate structural biology and drug discovery research.

Can I use Biopython to analyze 3D structural data downloaded from the Protein Data Bank?▼

You can use Biopython in conjunction with the requests and rcsb-api dependencies to programmatically access, download, and analyze 3D structural data from the Protein Data Bank.

What are the limitations of using programmatic access for structural biology data retrieval?▼

Limitations depend on the RCSB API query complexity and rate limits, meaning highly complex structural biology data retrieval requests may require pagination or refined search parameters to process successfully.

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