drug-db-pdb

Searching the RCSB PDB for drug discovery uses the RCSB Search API to return top-scoring PDB entries by keyword, filtered by organism, resolution, and experimental method. It then optionally enumerates bound ligand metadata from non-polymer entities.

Yes, downloading mmCIF coordinate files and validation reports from the Protein Data Bank is supported. The workflow retrieves entry metadata and can optionally download preferred mmCIF or PDB format coordinate files alongside wwPDB full validation report PDFs.

Retrieving PDB entries for macromolecular structures fetches entry core metadata including the title, experimental method, resolution, release dates, and unit cell parameters to support quality-aware selection for drug-discovery modeling.

Querying protein-ligand complex data through the RCSB Search API enforces rate limiting with retries and backoff. This ensures stable automated retrieval of macromolecular structure metadata and optional coordinate downloads during drug-discovery workflows.

Filtering PDB structures by resolution and experimental method for drug-target modeling is handled through the RCSB Search API. You can apply constraints like X-ray diffraction with resolution thresholds, such as less than 2.5 Å, and export results to JSON.

Selecting PDB entries for drug discovery workflows should use a quality-aware approach based on validation and ligand-quality data rather than resolution alone. The workflow retrieves wwPDB validation PDFs and ligand metadata to inform this selection.