pdb-database

Search and retrieve 3D protein and nucleic acid structures from RCSB Protein Data Bank.

Updated Dec 17, 2025

Search Tags:#protein structure #structural biology #3D structure #RCSB PDB #nucleic acid structure

Ready to run

npx skills add https://github.com/robotlearning123/claude-scientific-skills --skill pdb-database-robotlearning123

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: pdb-database
Source: https://github.com/robotlearning123/claude-scientific-skills/tree/main/scientific-skills/pdb-database
Command: npx skills add https://github.com/robotlearning123/claude-scientific-skills --skill pdb-database-robotlearning123

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill allows for efficient searching, retrieving, and analyzing 3D protein and nucleic acid structures from the RCSB Protein Data Bank, enabling users to perform a wide range of tasks in structural biology and drug discovery.

Core Features & Use Cases

Structure Search: Search for structures by text, sequence, or structure similarity.
Data Retrieval: Download coordinate files and retrieve metadata for specific structures.
Use Case: A researcher looking for high-resolution structures of a specific protein can use this Skill to quickly find and download the necessary data for further analysis.

Quick Start

Use the pdb-database skill to search for structures containing the sequence 'hemoglobin'.

Frequently Asked Questions about pdb-database

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

FAQPage Schema

How do I search for 3D protein structures from the RCSB PDB?▼

You can retrieve 3D protein structures from the RCSB PDB by performing text, sequence, or structure similarity searches to find specific coordinate files and metadata.

Can I find nucleic acid structures using sequence similarity searches?▼

Yes, sequence similarity searches support retrieving both 3D protein and nucleic acid structures, allowing you to identify matching entries from the RCSB Protein Data Bank.

How do I download coordinate files for structural biology analysis?▼

You can download coordinate files by searching for specific 3D structures and retrieving the associated data directly, providing the necessary inputs for structural biology and drug discovery tasks.

Do I need the rcsb-api to access RCSB PDB data?▼

Yes, the rcsb-api dependency is required to access RCSB PDB data, enabling the retrieval of 3D protein and nucleic acid structures and their metadata.

What is the best way to retrieve high-resolution structures for drug discovery?▼

The best way to retrieve high-resolution structures for drug discovery is using text, sequence, or structure similarity searches to find and download specific 3D coordinate files from the database.

How do I get metadata for a specific protein structure?▼

You can retrieve metadata for a specific protein structure by executing a targeted search, which provides access to detailed structural data alongside the downloadable coordinate files.