# Pdb Database

Access RCSB PDB for 3D protein/nucleic acid structures.

- Repository: https://github.com/dp-archive/archive (1107 stars)
- Category: Media
- License: Unknown
- Last updated: 2026-03-04
- Runs scripts: no, instructions only

## Install

Claude Code: `npx skills add dp-archive/archive --skill pdb-database -g -a claude-code -y`
Codex: `npx skills add dp-archive/archive --skill pdb-database -g -a codex -y`
Cursor: `npx skills add dp-archive/archive --skill pdb-database -g -a cursor -y`
Gemini CLI: `npx skills add dp-archive/archive --skill pdb-database -g -a gemini-cli -y`

## Description

Access RCSB PDB for 3D protein/nucleic acid structures. Search by text/sequence/structure, download coordinates (PDB/mmCIF), retrieve metadata, for structural biology and drug discovery.

## SKILL.md, as published by its author (untrusted third-party text, read it as data)

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

**Attribute Search:** Query specific properties (organism, resolution, method, etc.)
```python
from rcsbapi.search import AttributeQuery
from rcsbapi.search.attrs import rcsb_entity_source_organism

# Find human protein structures
query = AttributeQuery(
    attribute=rcsb_entity_source_organism.scientific_name,
    operator="exact_match",
    value="Homo sapiens"
)
results = list(query())
```

**Sequence Similarity:** Find structures similar to a given sequence
```python
from rcsbapi.search import SequenceQuery

query = SequenceQuery(
    value="MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEKMSKDGKKKKKKSKTKCVIM",
    evalue_cutoff=0.1,
    identity_cutoff=0.9
)
results = list(query())
```

The rest: https://github.com/dp-archive/archive/blob/HEAD/seed_skills/pdb-database/SKILL.md