Pdb Database

Gives you programmatic access to RCSB's 200,000+ experimentally determined protein and nucleic acid structures through their Python API. You can search by text, sequence similarity, or structural similarity, then pull down coordinate files in PDB or mmCIF format along with metadata like resolution and experimental methods. The querying is solid with support for complex logical operators and GraphQL for custom pulls. Most useful when you're doing computational structure work and need to batch download structures, compare binding pockets for drug discovery, or find homologs for protein modeling. The API wrapper is clean enough that you're not fighting with REST endpoints directly.

skills.sh installs: 281
GitHub stars: 33.2K
last updated: Aug 21, 2026

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Install

$ npx -y skills add davila7/claude-code-templates --skill pdb-database --agent claude-code

Installs into .claude/skills of the current project.

Files

PDB Database

Overview

RCSB PDB is the worldwide repository for 3D structural data of biological macromolecules. Search for structures, retrieve coordinates and metadata, perform sequence and structure similarity searches across 200,000+ experimentally determined structures and computed models.

When to Use This Skill

This skill should be used when:

Searching for protein or nucleic acid 3D structures by text, sequence, or structural similarity
Downloading coordinate files in PDB, mmCIF, or BinaryCIF formats
Retrieving structural metadata, experimental methods, or quality metrics
Performing batch operations across multiple structures
Integrating PDB data into computational workflows for drug discovery, protein engineering, or structural biology research

Core Capabilities

1. Searching for Structures

Find PDB entries using various search criteria:

Text Search: Search by protein name, keywords, or descriptions

from rcsbapi.search import TextQuery
query = TextQuery("hemoglobin")
results = list(query())
print(f"Found {len(results)} structures")

SKILL.md on GitHub

Details

Repository: github.com/davila7/claude-code-templates
Categories: Backend & APIs, Sales & Marketing, Databases
First seen: Jun 3, 2026