db-pdb

Name: db-pdb
Availability: InStock
Author: biomaps-infra

Search and download 3D protein structures from the RCSB PDB database.

Updated Mar 13, 2026

Search Tags:#protein structure #drug discovery #data retrieval #pdb #rcsb #structural biology

Ready to run

npx skills add https://github.com/biomaps-infra/blender-opencode --skill db-pdb

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: db-pdb
Source: https://github.com/biomaps-infra/blender-opencode/tree/main/.opencode/skills/db-pdb
Command: npx skills add https://github.com/biomaps-infra/blender-opencode --skill db-pdb

SYSTEM DOCUMENTATION & REQUIREMENTS

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

What problem does it solve?

This Skill provides access to the RCSB Protein Data Bank, enabling users to find, download, and analyze 3D structures of proteins and nucleic acids, crucial for structural biology and drug discovery.

Core Features & Use Cases

Search Structures: Find PDB entries by text, sequence, or structural similarity.
Download Data: Retrieve coordinate files (PDB, mmCIF) and metadata.
Analyze Structures: Parse and extract information from downloaded structure files.
Use Case: A researcher needs to find all human protein structures with a resolution better than 2.0 Å to study a specific disease pathway.

Quick Start

Use the db-pdb skill to search for human protein structures with a resolution less than 2.0 Angstroms.

Frequently Asked Questions about db-pdb

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

FAQPage Schema

How do I download 3D protein structures from the RCSB PDB database?▼

To download 3D protein structures from the RCSB PDB database, you can use this Skill to retrieve coordinate files in PDB or mmCIF formats by searching for specific entries via text, sequence, or structural similarity.

Can I search for PDB entries by sequence or structural similarity?▼

Yes, you can search PDB entries by sequence or structural similarity, enabling you to find related 3D protein and nucleic acid structures for structural biology and drug discovery applications.

What's the best way to find human protein structures with a specific resolution?▼

The best way to find human protein structures with a specific resolution is to perform a text search filtering by organism and resolution parameters, retrieving matching structural metadata and coordinate files.

How do I retrieve and parse metadata for structural biology applications?▼

You can retrieve and parse metadata for structural biology applications by accessing the RCSB PDB database programmatically, downloading coordinate files, and extracting information using integrated Python libraries like Biopython.

Does this RCSB PDB search tool support mmCIF format?▼

Yes, this RCSB PDB search tool supports downloading coordinate files in both PDB and mmCIF formats, allowing you to retrieve structural data according to your specific analysis requirements.

Do I need Biopython to analyze downloaded protein structure files?▼

You need Biopython to parse and extract information from downloaded protein structure files, as the Skill integrates this Python library to enable structural analysis of the retrieved 3D coordinates.