pdb-database

Name: pdb-database
Availability: InStock
Author: OwnLab

Query PDB structures and metadata via RCSB REST and GraphQL APIs.

21|1|Updated Mar 19, 2026

Search Tags:#search #metadata #structure #download #pdb #rcsb

Ready to run

npx skills add https://github.com/OwnLabAI/ownlab --skill pdb-database-ownlabai

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: pdb-database
Source: https://github.com/OwnLabAI/ownlab/tree/main/mart/skills/scientific-skills/pdb-database
Command: npx skills add https://github.com/OwnLabAI/ownlab --skill pdb-database-ownlabai

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

Access to the RCSB PDB data ecosystem is often scattered across REST, GraphQL, and file downloads; this skill unifies search, retrieval, and downloading of structures and metadata for structural biology workflows.

Core Features & Use Cases

Text, attribute, sequence, and structure searches to locate relevant PDB entries.
Retrieve entry-level data, polymer entities, assemblies, and metadata such as resolution and deposition dates.
Download structure files in PDB/mmCIF formats and access related data like FASTA sequences and biological assemblies.
Support batch operations and GraphQL-based queries for flexible data access.

Quick Start

Query PDB data, retrieve entry metadata, and download coordinates using the API.

Frequently Asked Questions about pdb-database

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

FAQPage Schema

How do I search and download PDB structures from the RCSB database?▼

You can search and download PDB structures by querying the RCSB API through unified REST and GraphQL endpoints, retrieving entry-level data, metadata, and structure files in PDB or mmCIF formats.

Can I retrieve entry metadata like resolution and deposition dates in batch from the RCSB PDB?▼

Yes, batch operations are supported to retrieve entry-level metadata, polymer entities, and assemblies, allowing you to process multiple PDB structures and their associated metadata simultaneously.

What's the best way to access biological assemblies and FASTA sequences for PDB entries?▼

Accessing biological assemblies and FASTA sequences is handled through GraphQL-based queries and file downloads, unifying data retrieval from the scattered RCSB PDB data ecosystem into a single workflow.

Does this approach to PDB data retrieval support both REST and GraphQL endpoints?▼

Yes, PDB data retrieval supports both REST and GraphQL endpoints, providing flexible data access for structural biology workflows while outlining common usage patterns, limits, and retry strategies.

What types of searches can I perform to locate relevant PDB structures?▼

You can perform text, attribute, sequence, and structure searches to locate relevant PDB entries, enabling comprehensive discovery of structural biology data across the RCSB database.

Are there limits or retry strategies when downloading mmCIF files from the RCSB API?▼

Yes, the skill outlines common usage patterns, limits, and retry strategies for downloading mmCIF and PDB files, ensuring reliable access to structure coordinates and related data.