search_pdb_entity
Search PDBj to find macromolecular structures, chemical components, or biologically interesting molecules. Filter by experimental method, resolution, ligand, and more, with detailed results per hit.
Instructions
Search PDBj for structures, chemical components, or BIRD molecules.
Returns rich, named fields per hit (not just the title) — for pdb,
each result carries the experimental method, resolution, bound ligands,
and citation; for cc, the formula, SMILES, and InChI.
RETURNS a JSON string {"total": int | null, "results": [ {…fields…} ]}.
total is null when PDBj gives no count (typical for structured-filter
searches) — that is NOT zero and does NOT mean "no results"; consult
results directly. On upstream/HTTP failure returns a JSON object with an
error key instead — CHECK FOR error BEFORE reading results.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| db | Yes | The database to search in. Allowed values are: - "pdb" (Protein Data Bank, macromolecular structures) - "cc" (Chemical Component Dictionary, ligands / small molecules) - "prd" (BIRD, Biologically Interesting Reference Molecule Dictionary, mostly peptides). | |
| name | No | ||
| term | No | ||
| limit | No | Max results to return, in [0, 500]. Default 20. | |
| query | No | Free-text keywords. May be empty when at least one structured filter is supplied. Accepts aliases: `search`, `term`, `keyword`, `keywords`, `search_term`, `name`. If both `query` and an alias are given with different values, this raises ValueError (pass only one). | |
| ligand | No | ||
| method | No | ||
| offset | No | Number of leading results to skip (server-side pagination). Default 0. | |
| search | No | ||
| smiles | No | ||
| source | No | ||
| formula | No | ||
| keyword | No | ||
| res_max | No | ||
| res_min | No | ||
| keywords | No | ||
| search_term | No |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| result | Yes |