pdb-database

name	pdb-database
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.
license	Unknown
metadata	{"skill-author":"K-Dense Inc."}
verified	false
lastVerifiedAt	"2026-02-19T05:29:09.098Z"
source	builtin
trust_score	100
provenance_sha	b1a9f5d8aafb1485

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")

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

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

from rcsbapi.search import SequenceQuery

query = SequenceQuery(
    value="MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVREIRKHKEKMSKDGKKKKKKSKTKCVIM",
    evalue_cutoff=,
    identity_cutoff=
)
results = (query())