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pdb-database

Query RCSB PDB protein and nucleic structures via the rcsb-api Python SDK.

298|27|Updated Feb 18, 2026
Search Tags:#protein structure#database query#pdb#rcsb#structural biology#macromolecular data
One-click install
npx skills add https://github.com/jaechang-hits/SciAgent-Skills --skill pdb-database-jaechang-hits
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: pdb-database
Source: https://github.com/jaechang-hits/SciAgent-Skills/tree/main/skills/structural-biology-drug-discovery/pdb-database
Command: npx skills add https://github.com/jaechang-hits/SciAgent-Skills --skill pdb-database-jaechang-hits

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 (PDB), enabling users to search for and retrieve experimental 3D structural data of biological macromolecules.

Core Features & Use Cases

  • Structure Search: Find PDB entries using text, attribute filters, sequence similarity, or structure similarity.
  • Metadata Retrieval: Fetch detailed experimental and biological metadata for structures.
  • File Download: Download coordinate files (PDB, mmCIF) for further analysis.
  • Use Case: Identify all human kinase structures determined by X-ray crystallography with a resolution better than 2.0 Å.

Quick Start

Use the pdb-database skill to find PDB IDs for human kinases with 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 query the RCSB PDB database for protein structures programmatically?▼

You can query the RCSB PDB database for protein structures programmatically by using the rcsb-api Python SDK to search via text, attribute filters, sequence similarity, or structural similarity.

How do I download mmCIF or PDB coordinate files for biological macromolecules?▼

To download coordinate files for biological macromolecules, you can use the PDB query skill to retrieve and download experimental structural data in PDB or mmCIF formats for further analysis.

Can I search for protein structures in the PDB by resolution and experimental method?▼

Yes, you can search for protein structures in the PDB by resolution and experimental method using attribute filters, such as finding human kinase structures determined by X-ray crystallography with a resolution better than 2.0 Å.

What is the best way to fetch experimental and biological metadata for PDB entries?▼

The best way to fetch experimental and biological metadata for PDB entries is to use the rcsb-api Python SDK, which enables programmatic retrieval of detailed structural and experimental information.

Does the PDB database query skill support sequence similarity searches for nucleic acid structures?▼

Yes, the PDB database query skill supports sequence similarity searches for both protein and nucleic acid structures, along with text, attribute, and structural similarity search options.

Do I need biopython to retrieve macromolecular data from the RCSB PDB?▼

Yes, biopython is a required dependency alongside the rcsb-api and requests libraries to programmatically query the RCSB PDB and retrieve macromolecular data.

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