pdb-databaselisted
Install: claude install-skill aiskillstore/marketplace
# 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())
``