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pdb-database

Retrieve 3D structural data from the RCSB PDB repository via GraphQL and REST APIs.

16|7|Updated Nov 20, 2025
Search Tags:#structure#PDB#mmCIF#BioPython#rcsb
One-click install
npx skills add https://github.com/jackspace/ClaudeSkillz --skill pdb-database
Or copy as Structured Prompt for Agent▼
Please help me install this Agent Skill.
Skill: pdb-database
Source: https://github.com/jackspace/ClaudeSkillz/tree/main/skills/scientific-db-pdb-database
Command: npx skills add https://github.com/jackspace/ClaudeSkillz --skill pdb-database

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires rcsb-api, requests, and includes references (resource) components.

What problem does it solve?

Access RCSB PDB structures and metadata to support structural biology, drug discovery, and computational analyses.

Core Features & Use Cases

  • Searching for structures by text, sequence, or similarity
  • Downloading coordinate files (PDB/mmCIF)
  • Retrieving structure metadata (resolution, organism, method)
  • Batch operations for multiple structures
  • GraphQL and scripted data access patterns

Quick Start

Install the official RCSB PDB Python API client and fetch a simple entry:

  1. pip install rcsb-api
  2. from rcsbapi.data import fetch, Schema data = fetch("4HHB", schema=Schema.ENTRY)

Frequently Asked Questions about pdb-database

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

FAQPage Schema
How do I download 3D protein structures from the PDB database?▼

Download 3D protein structures from PDB using the RCSB API by fetching entries in PDB, mmCIF, or BinaryCIF formats. Install rcsb-api, import the fetch function with your desired schema, and retrieve coordinate files for structural analysis and visualization.

Can I search the PDB database by protein sequence or structure similarity?▼

The RCSB PDB supports text, sequence, and structure similarity searches through programmatic GraphQL and REST interfaces. Query by amino acid sequence, structural motifs, or text metadata to locate homologous proteins and related structures across the repository.

What metadata can I retrieve for PDB structures?▼

Retrieve comprehensive metadata including resolution, experimental method, organism source, publication references, and functional annotations. The RCSB API provides structured access to entry-level and assembly-level metadata for filtering and comparative analysis.

How do I batch process multiple PDB structures for drug discovery workflows?▼

Process multiple structures in batch using programmatic access patterns with the RCSB API and requests library. Automate coordinate downloads, metadata extraction, and analysis pipelines across sets of structures for high-throughput drug discovery and structural screening.

Does the PDB API support both REST and GraphQL queries?▼

Yes, the RCSB PDB provides both GraphQL and REST data access patterns. Choose GraphQL for flexible, schema-driven queries or REST for simpler endpoint-based requests depending on your workflow complexity and integration requirements.

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