pdb-database
PDB Database
Overview
RCSB PDB is the worldwide repository for 3D structural data of biological macromolecules with 200,000+ experimentally determined structures. The rcsb-api Python SDK provides unified access to Search API (find PDB IDs by text, attributes, sequence, or structure similarity) and Data API (retrieve metadata and coordinates). Use this skill for programmatic structural biology queries, drug target analysis, and protein family comparisons.
When to Use
- Searching for protein or nucleic acid crystal/cryo-EM/NMR structures by keyword or property
- Finding structures similar to a query sequence (MMseqs2) or 3D geometry (BioZernike)
- Retrieving experimental metadata (resolution, method, organism, deposition date) for structure sets
- Downloading coordinate files (PDB, mmCIF) for molecular dynamics, docking, or visualization
- Building structure-based datasets for machine learning or drug discovery pipelines
- Comparing protein-ligand complexes across a target family
- For AlphaFold predicted structures, use
alphafold-database-accessinstead - For protein sequence/annotation queries without structures, use
uniprot-protein-databaseinstead
Prerequisites
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