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pdb-database

Search RCSB PDB structures by sequence or attributes and download coordinate files.

21|2|Updated Dec 8, 2025
Search Tags:#drug discovery#pdb#batch retrieval#structural biology#sequence search#mmcif download#structural metadata
One-click install
npx skills add https://github.com/silverstein/claude-scientific-skills-desktop --skill pdb-database-silverstein
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: pdb-database
Source: https://github.com/silverstein/claude-scientific-skills-desktop/tree/main/corpus/pdb-database
Command: npx skills add https://github.com/silverstein/claude-scientific-skills-desktop --skill pdb-database-silverstein

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

Getting from a scientific question about a protein or nucleic acid to the exact 3D structures and metadata you need is slow and error-prone. This Skill helps you locate relevant PDB/mmCIF entries and retrieve the precise coordinate files and quality details required for downstream structural biology or drug discovery work.

Core Features & Use Cases

  • Structure search by text, attributes, and sequence similarity (including sequence and 3D structure similarity) to rapidly narrow candidates.
  • Targeted retrieval of entry, polymer-entity, and assembly metadata for method, resolution, and experimental context.
  • Coordinate downloads in multiple formats (PDB, mmCIF, and biological assemblies) to support modeling, analysis, and visualization pipelines.
  • Batch workflows for processing multiple PDB IDs with consistent fetching and metadata extraction.
  • Python API integration using the RCSB PDB Python client for programmatic use in automated pipelines.

Quick Start

Use the PDB database to search for a protein structure and then download its mmCIF coordinates and metadata for your drug discovery workflow.

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 mmCIF files and structural metadata from the PDB database?▼

Batch download mmCIF files and structural metadata by processing multiple PDB IDs with consistent fetching using the RCSB PDB Python API client, yielding coordinate files and experimental context for automated pipelines.

Can I search for PDB structures using sequence similarity for protein engineering workflows?▼

Search PDB structures by sequence similarity to rapidly narrow protein candidates, retrieving exact 3D coordinate files and quality details required for downstream structural biology and protein engineering analysis.

What's the best way to retrieve biological assemblies from RCSB PDB for structure-based drug discovery?▼

Retrieve biological assemblies from RCSB PDB by selecting specific assembly formats during coordinate download, ensuring accurate downstream structure-based drug discovery and visualization pipeline results.

Does this PDB search method support filtering by experimental method and resolution attributes?▼

Filtering by experimental method and resolution attributes is supported during structure search, allowing targeted retrieval of entry, polymer-entity, and assembly metadata for precise structural biology context.

How do I find PDB entries by 3D structure similarity rather than text queries?▼

Find PDB entries by 3D structure similarity to locate relevant protein or nucleic-acid structures beyond text queries, retrieving exact coordinate files and quality details for downstream analysis.

Why do I need to select biological assemblies when downloading PDB coordinate files?▼

Selecting biological assemblies during PDB coordinate file download ensures you retrieve the functional oligomeric state of the macromolecule, preventing inaccurate downstream structural biology and modeling results.

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