pdb-database

Name: pdb-database
Availability: InStock
Author: robinbarvaag

Search and retrieve 3D protein and nucleic acid structures from RCSB PDB.

Updated Jan 10, 2026

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

Ready to run

npx skills add https://github.com/robinbarvaag/poynt --skill pdb-database-robinbarvaag

💬 Prompt for ChatGPT / Claude Chat▼

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

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 search for, retrieve, and analyze 3D structural data of biological macromolecules, streamlining research in structural biology and drug discovery.

Core Features & Use Cases

Search Structures: Find proteins and nucleic acids by text, sequence, or structural similarity.
Retrieve Data: Download coordinate files (PDB, mmCIF) and fetch detailed metadata.
Use Case: A researcher needs to find all human hemoglobin structures resolved below 2.0 Å resolution and download their PDB files for further analysis.

Quick Start

Use the pdb-database skill to search for human hemoglobin structures with a resolution less than 2.0 Å and list their PDB IDs.

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 protein structures from the RCSB PDB?▼

You can search and download protein structures from the RCSB PDB by using this skill to find proteins by text, sequence, or structural similarity and retrieve coordinate files like PDB and mmCIF formats.

How do I retrieve 3D macromolecular structures for drug discovery workflows?▼

To retrieve 3D macromolecular structures for drug discovery, search the RCSB PDB programmatically to fetch detailed metadata and download coordinate files needed for structural biology analysis.

Can I filter RCSB PDB searches by resolution and download the coordinate files?▼

Yes, you can filter RCSB PDB searches by specific criteria like resolution below 2.0 Å, list the matching PDB IDs, and directly download their corresponding coordinate files.

What is the best way to programmatically access RCSB PDB data for structural biology?▼

The best way to programmatically access RCSB PDB data for structural biology is leveraging the rcsb-api Python package to query and retrieve 3D structural data of biological macromolecules.

Does this protein structure retrieval skill require biopython and requests dependencies?▼

Yes, this protein structure retrieval skill requires biopython, requests, and the rcsb-api Python packages to interact with PDB data and execute search functionalities.

What are the limitations of using rcsb-api for nucleic acid structure data retrieval?▼

The rcsb-api facilitates searching and retrieving 3D protein and nucleic acid structures, but complex structural similarity queries may require additional downstream processing using biopython.