pdb-database

Topics in the source

• PDB Database
• Overview
• When to Use This Skill
• Core Capabilities
• 1. Searching for Structures
• 2. Retrieving Structure Data
• 3. Downloading Structure Files
• 4. Working with Structure Data

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. 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 Find PDB entries using various search criteria: Text Search: Search by protein name, keywords, or descriptions Attribute Search: Query specific properties (organism, resolution, method, etc.) Sequence Similarity: Find structures similar to a given sequence Structure Similarity: Find structures with similar 3D geometry Combining Queries: Use logical operators to build complex searches Access detailed information about specific PDB entries: Basic Entry Information: Polymer Entity I

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