alterlab-pdb

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.

Scripts

scripts/query_pdb.py — RCSB Search + Data + file APIs (stdlib only, JSON to stdout):

python scripts/query_pdb.py search hemoglobin --rows 25     # full-text search (entry IDs)
python scripts/query_pdb.py entry 4HHB                      # entry metadata
python scripts/query_pdb.py download 4HHB --format cif      # download coordinates

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")

Attribute Search: Query specific properties (organism, resolution, method, etc.)

from rcsbapi.search import AttributeQuery
from rcsbapi.search import search_attributes as attrs

# Find human protein structures (idiomatic form — recommended)
query = attrs.rcsb_entity_source_organism.scientific_name == "Homo sapiens"
results = list(query())

# OR explicit AttributeQuery with a dotted-path STRING (not the Attr object):
query = AttributeQuery(
    attribute="rcsb_entity_source_organism.scientific_name",
    operator="exact_match",
    value="Homo sapiens",
)
results = list(query())