pdb-database

Search and retrieve 3D protein structures from RCSB PDB via rcsbapi.

8|Updated Jan 13, 2026

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

Ready to run

npx skills add https://github.com/hxk622/TokenDance --skill pdb-database-hxk622

💬 Prompt for ChatGPT / Claude Chat▼

Please help me install this Agent Skill.
Skill: pdb-database
Source: https://github.com/hxk622/TokenDance/tree/main/backend/app/skills/builtin/scientific/database/pdb-database
Command: npx skills add https://github.com/hxk622/TokenDance --skill pdb-database-hxk622

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 programmatic access to the RCSB Protein Data Bank, enabling users to search for, retrieve, and download 3D structural data of biological macromolecules.

Core Features & Use Cases

Structure Searching: Find proteins and nucleic acids by text, sequence, or structural similarity.
Data Retrieval: Download coordinate files (PDB, mmCIF) and retrieve detailed metadata.
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. This Skill can perform that search and download the relevant PDB files.

Quick Start

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

Frequently Asked Questions about pdb-database

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

FAQPage Schema

How do I retrieve 3D protein structures in mmCIF format from the RCSB PDB?▼

To retrieve 3D protein structures in mmCIF format, use this Skill to query the RCSB PDB via the rcsb-api package. It programmatically downloads coordinate files and fetches structural biology metadata for drug discovery workflows.

Can I search for human protein structures with a specific resolution limit using the RCSB API?▼

Yes, you can search for human protein structures with a specific resolution limit. The Skill executes structural queries against the RCSB PDB, filtering macromolecules by attributes like organism and resolution threshold to return matching entries.

Does this RCSB PDB search tool require BioPython to fetch nucleic acid coordinate files?▼

BioPython is listed as a dependency for this Skill. It facilitates downloading coordinate files and fetching metadata for nucleic acid structures alongside the required rcsb-api and requests packages to execute data retrieval.

What is the best way to programmatically access structural biology data for drug discovery?▼

The best way to programmatically access structural biology data is using this Skill's rcsb-api integration. It searches the RCSB PDB for 3D macromolecular structures and retrieves coordinate files to support drug discovery workflows.

Are there limitations to searching for structural similarity using the rcsb-api package?▼

The Skill supports searching by structural similarity via the rcsb-api package. It retrieves matching 3D structures and metadata, though complex structural biology similarity queries may require downloading full coordinate files for local analysis.

How do I download PDB coordinate files for nucleic acids to study a disease pathway?▼

You can download PDB coordinate files for nucleic acids by querying the RCSB PDB. The Skill searches for relevant structures and retrieves the files needed to study structural components of a specific disease pathway.