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pdb-database

Search and retrieve PDB/mmCIF coordinate files from RCSB PDB.

1.1k|99|Updated Feb 12, 2026
Search Tags:#bioinformatics#protein structure#drug discovery#data retrieval#pdb#structural biology
One-click install
npx skills add https://github.com/MooseGoose0701/skill-compose --skill pdb-database-moosegoose0701
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: pdb-database
Source: https://github.com/MooseGoose0701/skill-compose/tree/main/skills/pdb-database
Command: npx skills add https://github.com/MooseGoose0701/skill-compose --skill pdb-database-moosegoose0701

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.

Core Features & Use Cases

  • Structure Search: 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 with a resolution better than 2.0 Å to study a specific disease pathway. This Skill can perform that search and download the relevant PDB files.

Quick Start

Use the pdb-database skill to search for human hemoglobin structures and download their PDB files.

Frequently Asked Questions about pdb-database

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

FAQPage Schema
How do I programmatically search the RCSB PDB for protein structures?▼

You can programmatically search the RCSB PDB for protein structures by utilizing text, sequence, or structural similarity queries to find specific biological macromolecules.

How do I download mmCIF and PDB coordinate files for structural biology analysis?▼

You can download mmCIF and PDB coordinate files by executing retrieval commands that fetch structural data and detailed metadata directly from the RCSB database.

Can I filter RCSB PDB searches by resolution for drug discovery applications?▼

Yes, you can filter RCSB PDB searches by specific parameters like resolution to find high-quality structures suitable for drug discovery and disease pathway analysis.

Does this PDB data retrieval approach work with BioPython?▼

Yes, this PDB data retrieval approach integrates seamlessly with BioPython, enabling you to perform structural analysis on the downloaded protein and nucleic acid coordinate files.

What is the best way to retrieve 3D nucleic acid structures from the Protein Data Bank?▼

The best way to retrieve 3D nucleic acid structures is to use programmatic RCSB API access to query the database and download the relevant coordinate files.

Are there limitations to using the rcsb-api package for protein structure similarity searches?▼

The rcsb-api package facilitates protein structure similarity searches and metadata retrieval, but complex structural analysis requires post-processing with BioPython after downloading the coordinate files.

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