pdb-database

Search PDB structures and download coordinates and metadata via REST or GraphQL.

52|6|Updated Nov 24, 2025

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

Ready to run

npx skills add https://github.com/ovachiever/droid-tings --skill pdb-database-ovachiever

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: pdb-database
Source: https://github.com/ovachiever/droid-tings/tree/main/skills/pdb-database
Command: npx skills add https://github.com/ovachiever/droid-tings --skill pdb-database-ovachiever

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

This Skill enables researchers to quickly locate PDB entries, retrieve coordinates and structural metadata, and batch-operate on multiple structures, saving hours of manual web searches and downloads.

Core Features & Use Cases

Search & Retrieve: Find PDB entries by text, sequence, or structure and fetch coordinates (PDB/mmCIF) and metadata.
Batch Operations: Run searches and downloads across multiple structures in one workflow.
Metadata Retrieval: Extract key details such as resolution and experimental method for quality assessment.
Use Case: Build a pipeline that gathers coordinates and metadata for a set of targets for docking and modeling workflows.

Quick Start

Use the pdb-database skill to search for "hemoglobin" and download the corresponding 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 search and download PDB protein structures?▼

Search PDB structures by text, sequence, or structure similarity, then download coordinates in PDB, mmCIF, or BinaryCIF formats along with metadata like resolution and experimental method for immediate use in computational pipelines.

Can I batch download multiple PDB files and metadata at once?▼

Yes, run batch operations across multiple PDB structures in a single workflow to retrieve coordinates and metadata simultaneously, eliminating manual downloads for large structure sets.

What data formats does PDB structure retrieval support?▼

PDB structure retrieval supports PDB, mmCIF, and BinaryCIF formats via REST and GraphQL APIs, enabling flexible integration into drug discovery and computational modeling workflows.

How do I use PDB structure data in drug discovery workflows?▼

Integrate PDB coordinates and metadata directly into docking and modeling pipelines by querying, downloading, and parsing structures with quality metrics for automated computational analysis.

Does PDB structure search work with sequence and structure similarity queries?▼

Yes, search by text, attribute, sequence, or structure similarity to find relevant PDB entries, enabling flexible discovery based on protein sequence alignment or 3D structural comparison.

What metadata can I extract from PDB entries?▼

Retrieve key structural metadata including resolution, experimental method, and other quality indicators to assess and filter PDB entries before integration into analysis workflows.