pdb-database

Name: pdb-database
Availability: InStock
Author: rubensliv

Search, download, and analyze PDB structures via REST or GraphQL.

15|2|Updated Dec 17, 2025

Search Tags:#metadata #download #pdb #drug-discovery #structure-search #rcsb #biostructure

Ready to run

npx skills add https://github.com/rubensliv/k-dense-ai --skill pdb-database-rubensliv

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: pdb-database
Source: https://github.com/rubensliv/k-dense-ai/tree/main/scientific-skills/pdb-database
Command: npx skills add https://github.com/rubensliv/k-dense-ai --skill pdb-database-rubensliv

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

Researchers need quick access to 3D structural data, coordinates, and rich metadata from the RCSB PDB without manual, scattered searches.

Core Features & Use Cases

Search for protein and nucleic acid structures by text, sequence, or structural similarity.
Download coordinates in PDB or mmCIF formats and fetch comprehensive metadata (structure title, experimental method, resolution, deposition date).
Perform batch queries across multiple structures and integrate PDB data into computational workflows for drug discovery, protein engineering, and structural biology analysis.

Quick Start

Query a structure by name and download its PDB file.

Frequently Asked Questions about pdb-database

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

FAQPage Schema

How do I download PDB structures and extract metadata for bioinformatics workflows?▼

You can search RCSB PDB by text, sequence, or structural similarity to retrieve 3D biostructure coordinates and metadata, eliminating the need for manual scattered searches across the database.

Can I perform batch queries to download multiple PDB files at once?▼

Yes, batch querying across multiple structures is supported, enabling you to programmatically retrieve and integrate large sets of PDB coordinates and metadata into drug discovery or protein engineering pipelines.

Does this tool support retrieving structures via GraphQL and REST APIs?▼

Yes, structure retrieval and metadata extraction are supported through both REST and GraphQL interfaces, allowing flexible integration of PDB structural data into your custom computational analysis workflows.

What is the best way to search for protein structures by sequence or structural similarity?▼

Searching RCSB PDB supports text, sequence, and structure-based similarity queries to pinpoint relevant biostructures, streamlining access to 3D coordinates and experimental metadata for downstream analysis.

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

Downloading structures in mmCIF format is necessary for large complexes exceeding PDB format limits or when richer metadata parsing is required for complex bioinformatics and drug discovery workflows.