pdb-database

Retrieve PDB structures and metadata via RCSB PDB API queries.

1|Updated Mar 4, 2026

Search Tags:#bioinformatics #metadata #download #pdb #structure-search #rcsb

Ready to run

npx skills add https://github.com/Hung-3008/agusta --skill pdb-database-hung-3008

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: pdb-database
Source: https://github.com/Hung-3008/agusta/tree/main/.agents/skills/pdb-database
Command: npx skills add https://github.com/Hung-3008/agusta --skill pdb-database-hung-3008

SYSTEM DOCUMENTATION & REQUIREMENTS

💡 This Skill includes references (resource) components.

What problem does it solve?

Quickly access RCSB PDB structures, search by text, sequence, or structure, and retrieve coordinates and metadata for structural biology and drug discovery.

Core Features & Use Cases

Searching for Structures: Find PDB entries by text, sequence similarity, or structural similarity, and perform combined queries.
Downloading Structure Files: Retrieve coordinates in PDB, mmCIF, or BinaryCIF formats, including biological assemblies.
Retrieving Metadata: Access experimental methods, resolution, deposition dates, and other entry-level details.
Batch Operations: Process multiple structures efficiently for workflows and analyses.
Use Case: Integrate PDB data into computational pipelines for modeling, docking, or visualization.

Quick Start

Query a structure by ID or text, then download coordinates in PDB or mmCIF formats.

Frequently Asked Questions about pdb-database

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

FAQPage Schema

How do I retrieve PDB structure coordinates and metadata using the RCSB API?▼

You can retrieve PDB structures and metadata by querying the RCSB PDB API using text, sequence, or structural similarity searches. Coordinates are then downloadable in PDB, mmCIF, or BinaryCIF formats, including biological assemblies.

Can I download biological assemblies from the PDB in mmCIF format?▼

Yes, biological assemblies can be downloaded in mmCIF format. The Skill supports retrieving coordinate files in PDB, mmCIF, and BinaryCIF formats, including biological assemblies, for integration into structural biology workflows.

What is the best way to batch download PDB files for computational pipelines?▼

The best way to batch download PDB files is using the Skill's batch retrieval functionality to process multiple structures efficiently. This enables seamless integration of coordinates and metadata into computational pipelines for modeling, docking, or visualization.

Does the RCSB PDB API support sequence similarity searches for structural biology?▼

Yes, the RCSB PDB API supports sequence similarity searches for structural biology. You can find PDB entries by text, sequence similarity, or structural similarity, and perform combined queries to retrieve relevant structural data.

How do I access experimental methods and resolution data for a specific PDB entry?▼

To access experimental methods and resolution data for a specific PDB entry, use the metadata retrieval function. This provides entry-level details including deposition dates, experimental methods, and resolution for structural biology analysis.