pdb-database - Access RCSB PDB 3D Protein and Nucleic Acid Structures
Search, retrieve, and download 3D biological macromolecular structures and metadata from the RCSB PDB repository via text, sequence, or structural similarity queries.
Tags
Updated: 2026-06-30Capabilities
Typical Inputs
Typical Outputs
What this skill does
- search PDB structures by text
- search PDB by sequence similarity
- search PDB by structural similarity
- query PDB entries by attributes
- combine search queries with operators
- retrieve PDB entry metadata
- download PDB format coordinate files
- download mmCIF format coordinate files
- download biological assembly files
- fetch polymer entity information
- execute GraphQL queries on PDB
- batch process multiple PDB entries
- extract experimental method details
- retrieve resolution and quality metrics
Inputs
- PDB entry ID
- Search keywords or text query
- Protein or nucleic acid sequence
- Structure similarity search parameters
- Attribute query parameters
- GraphQL query string
Outputs
- PDB structure search result lists
- PDB format coordinate files
- mmCIF format coordinate files
- Structure metadata and experimental details
- Batch structure information reports
Requirements
- Python runtime environment
- rcsb-api Python package installed
- Internet access to RCSB PDB servers