QuantumPDB¶

QuantumPDB (qp) is a fully integrated, open-source Python package that automates the generation of quantum mechanical (QM) cluster models from protein structures. It takes raw PDB files and produces ready-to-run QM calculation inputs through a five-stage pipeline: structure preparation, protonation, cluster extraction, job management, and post-processing analysis.

QM cluster models capture the electronic structure of enzyme active sites by carving out a region of the protein surrounding the catalytic center. Unlike simple distance-based cutoffs, QuantumPDB uses Voronoi tessellation to construct hierarchical interaction spheres that faithfully capture the chemical environment, even for non-spherical active sites.