pdb-database

# 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()) ``...