pdb

name	pdb
description	3D protein structure search via RCSB PDB. Input MUST be a protein/gene name (e.g. 'KRAS', 'EGFR', 'BTK') or a 4-character PDB ID (e.g. '6OIM'). Returns zero results for drug/chemistry phrases such as 'covalent inhibitors' or 'warhead selectivity'. Strip all drug qualifiers and pass only the target protein name or PDB ID.
metadata	null

PDB - Protein Data Bank

Search and fetch protein structures from the RCSB Protein Data Bank.

Usage

Search for structures:

python3 {baseDir}/scripts/pdb_search.py --query "kinase human"

Get structure details:

python3 {baseDir}/scripts/pdb_search.py --pdb-id 1ATP

Search by sequence:

python3 {baseDir}/scripts/pdb_search.py --sequence "MTEYKLVVVGAGGVGKSALTIQLIQ" --identity 70

Parameters

Parameter	Description	Default
--query	Text search query	-
--pdb-id	Specific PDB ID to fetch	-
--sequence	Sequence for similarity search	-
--identity	Minimum sequence identity %	90
--max-results