db-pdb

Goal

To programmatically discover and retrieve protein (and protein-ligand complex) structures from the RCSB Protein Data Bank (PDB) by combining the RCSB Search API (to find matching PDB IDs) with the RCSB Data API (to retrieve rich metadata and ligand information), and optionally downloading coordinate files (PDB/mmCIF) and wwPDB validation reports for downstream modeling.

Instructions

1. (Recommended) Create a dedicated output directory

Keep downloaded coordinates/JSON in a reproducible folder.

# Env: base-agent
mkdir -p research/db-pdb/ace2_example

2. Search by keyword (full-text)

Uses the RCSB Search API to return the top scoring PDB IDs for a query.