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LeonChaoX
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pdb-database

Search RCSB PDB entries and download coordinates with metadata.

783|65|Updated Feb 27, 2026
Search Tags:#protein engineering#metadata retrieval#sequence similarity#structure search#mmcif download#rcsb pdb
One-click install
npx skills add https://github.com/LeonChaoX/qinyan-academic-skills --skill pdb-database-leonchaox
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: pdb-database
Source: https://github.com/LeonChaoX/qinyan-academic-skills/tree/main/skills/08-%E8%9B%8B%E7%99%BD%E8%B4%A8%E5%B7%A5%E7%A8%8B%E4%B8%8E%E7%BB%93%E6%9E%84%E7%94%9F%E7%89%A9%E5%AD%A6/pdb-database
Command: npx skills add https://github.com/LeonChaoX/qinyan-academic-skills --skill pdb-database-leonchaox

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

RCSB PDB information and structure files are difficult to locate, filter, and retrieve accurately across thousands of entries, which slows down protein engineering, structural biology, and drug discovery workflows.

Core Features & Use Cases

  • Structure Search (text/attributes/sequence/3D similarity): Find relevant PDB entries by keywords, organism or experimental attributes, sequence similarity, or structural similarity for downstream analysis.
  • Metadata Retrieval (quality, experimental method, resolution, dates): Pull entry-, entity-, and assembly-level details needed to judge dataset suitability and reproducibility.
  • Coordinate Download (PDB/mmCIF/BinaryCIF/assemblies): Download coordinates and assembly files for computational modeling, alignments, and structure-based comparisons.

Use Case: You want high-resolution human protein structures for modeling a binding site; you can search by organism and resolution, download the best candidates in mmCIF/PDB, and retrieve experimental method and quality metrics for selection.

Quick Start

Ask the AI to search RCSB PDB for Homo sapiens protein structures with resolution under 2.0 Å, then download the top 10 entries in mmCIF and return each entry’s title and experimental method.

Frequently Asked Questions about pdb-database

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

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

You can search RCSB PDB protein structures by filtering entries with specific text, attributes, organism, and resolution limits. This allows you to quickly identify and retrieve high-resolution human protein structures suitable for downstream computational modeling and binding site analysis.

Can I download mmCIF and PDB coordinate files in bulk?▼

Yes, you can download mmCIF, PDB, and BinaryCIF coordinate files in bulk. The skill handles multiple downloads and assemblies, enabling efficient batch dataset building for computational modeling, structural alignments, and structure-based comparisons.

What metadata fields can I retrieve from the RCSB PDB database?▼

You can retrieve entry-, entity-, and assembly-level metadata from the RCSB PDB database. Extracted fields include experimental method, resolution, deposit dates, release dates, and quality metrics needed to judge dataset suitability and reproducibility.

Does the RCSB API support sequence similarity and 3D structure search?▼

Yes, the RCSB API supports sequence similarity and 3D structural similarity searches. You can find relevant PDB entries by matching sequence similarity or structural similarity to query inputs for downstream structural biology research and drug discovery workflows.

What's the best way to build a high-resolution dataset for protein engineering?▼

The best way to build a high-resolution protein engineering dataset is to programmatically search RCSB PDB by organism and resolution, retrieve experimental method metadata, and download the best coordinate candidates in mmCIF format for computational analysis.

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