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pdb-database

Search RCSB PDB entries and download coordinates in PDB or mmCIF formats.

1|Updated Mar 11, 2026
Search Tags:#bioinformatics#metadata#pdb#structure-search#protein-structure#rcsb#mmcif
One-click install
npx skills add https://github.com/SciMate-AI/scicli --skill pdb-database-scimate-ai
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: pdb-database
Source: https://github.com/SciMate-AI/scicli/tree/main/internal/skills/bundled/claude-scientific-skills/skills/pdb-database
Command: npx skills add https://github.com/SciMate-AI/scicli --skill pdb-database-scimate-ai

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

Provide researchers with streamlined access to the RCSB PDB: search structures by text, sequence, or structure, and retrieve coordinates and metadata for downstream analysis.

Core Features & Use Cases

  • Text, attribute, sequence, and structure similarity searches to locate relevant structures
  • Download coordinates in PDB/mmCIF formats and access rich structural metadata
  • Batch operations across multiple entries to accelerate computational workflows
  • Use Case: assemble a curated set of high-resolution human protein structures for docking studies

Quick Start

Query the PDB to find structures by text, download coordinates, and retrieve metadata.

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 entries by protein sequence or structure similarity?▼

PDB structure search supports text, attribute, sequence, and structure similarity queries to locate relevant RCSB entries. You can retrieve matching structures and download their coordinate files for downstream computational workflows.

What's the best way to download multiple PDB coordinates in mmCIF or PDB format?▼

Batch operations support downloading coordinates across multiple PDB entries in either PDB or mmCIF formats. This accelerates computational workflows by assembling curated structural datasets for downstream analysis.

Can I retrieve structural metadata from the PDB for computational workflows?▼

You can fetch rich structural metadata for PDB entries to support downstream computational workflows. The skill provides REST and GraphQL access to retrieve detailed entry information alongside coordinate downloads.

Does the PDB search API support batch queries and rate-limiting guidance?▼

PDB database access supports batch queries across multiple entries and includes robust error handling with rate-limiting guidance. This ensures reliable retrieval of coordinates and metadata when automating computational workflows.

When do I need to download mmCIF format files instead of PDB format?▼

Download mmCIF format files when working with large complex structures that exceed traditional PDB format limitations, or when downstream workflows require richer metadata representation. Both coordinate formats are fully supported for retrieval.

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