query-pdb

Query the RCSB PDB database for protein structures by text, gene name, or method.

1|Updated Mar 12, 2026

Search Tags:#protein structure #pdb #rcsb #structural biology #cryo-em #nmr #x-ray diffraction

Ready to run

npx skills add https://github.com/yf8578/clawomics --skill query-pdb-yf8578

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: query-pdb
Source: https://github.com/yf8578/clawomics/tree/main/skills/query-pdb
Command: npx skills add https://github.com/yf8578/clawomics --skill query-pdb-yf8578

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill requires requests, and includes scripts (resource) components.

What problem does it solve?

This Skill helps users find and retrieve experimental protein structure data from the RCSB Protein Data Bank (PDB), addressing the need for information on protein conformations and molecular details.

Core Features & Use Cases

Structure Search: Query the PDB using keywords, gene names, or specific PDB IDs.
Data Retrieval: Obtain details like protein title, experimental method (X-ray, cryo-EM, NMR), and resolution.
Structure Download: Download PDB files for further analysis.
Use Case: A researcher needs to find the crystal structure of a specific human protein to understand its active site. They can use this Skill to search for the protein by its gene name and retrieve relevant PDB entries, including their resolution and method.

Quick Start

Use the query-pdb skill to search for the crystal structure of human insulin.

Frequently Asked Questions about query-pdb

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

FAQPage Schema

How do I find protein structures in the RCSB PDB database?▼

To find protein structures in the RCSB PDB database, you can query it using text, gene names, or specific PDB IDs to retrieve entries along with their experimental methods and structural details.

Can I search for experimental protein structures using a gene name?▼

Yes, you can search for experimental protein structures using a gene name. The system queries the RCSB PDB database to retrieve matching entries, including details like the protein title and experimental method.

How do I download PDB files for molecular modeling and drug discovery?▼

You can download PDB files for molecular modeling and drug discovery by querying the RCSB PDB database. The tool retrieves experimental structures and facilitates downloading the files for further analysis.

Does this tool require the requests library to query the RCSB PDB?▼

Yes, querying the RCSB PDB database requires the requests library. This dependency is necessary to handle the API interactions for retrieving protein structure data and downloading PDB files.

What structural details can I retrieve when I search for a protein structure?▼

When you search for a protein structure, you can retrieve structural details including the protein title, experimental method such as X-ray, cryo-EM, or NMR, and the resolution of the structure.

What's the best way to find a specific human protein crystal structure for active site analysis?▼

The best way to find a specific human protein crystal structure for active site analysis is to search the RCSB PDB by the protein's gene name to retrieve relevant PDB entries, resolution, and method.