---
id: pdb2pqr
version: "3.7.1"
license: Copyright (c) 2002-2024, Jens Erik Nielsen; Nathan A. Baker; Battelle Memorial Institute, Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific… (full text in the JSON record)
license_treatment: permissive
maintenance: active
---

# pdb2pqr — Automates many of the common tasks of preparing structures for continuum solvation calculations as well as many other types of biomolecular structure modeling, analysis, and simulation.

License: permissive · Maintenance: active · Downloads: 430.2K/mo

## What it is and what it does

PDB2PQR is a specialized tool for preparing protein structures from the Protein Data Bank for computational chemistry and molecular dynamics simulations. It automates common preprocessing steps including protonation state assignment, force field parameterization, and structure validation—tasks that would otherwise require manual intervention or multiple separate tools. The package wraps years of research in biomolecular structure preparation and integrates with the Poisson-Boltzmann ecosystem for continuum solvation modeling.

The package depends on docutils, mmcif-pdbx, numpy, propka, and requests to handle structure parsing, protonation prediction, numerical computation, and data retrieval. It runs as a command-line tool or Python library and is actively maintained with support for modern Python versions. The codebase is small enough to install quickly but mature enough for production use in research workflows.

Use it for:

- Prepare protein crystal structures for molecular dynamics simulations by assigning protonation states and force field parameters.
- Convert PDB files to PQR format for use in Poisson-Boltzmann electrostatics calculations.
- Batch-process multiple protein structures for high-throughput computational screening or binding studies.
- Validate and clean protein structures before submission to simulation packages or structure analysis pipelines.
- Automate protonation assignment at physiological pH for protein-ligand docking workflows.

## Worth the install?

AI-flagged interpretation of the facts above — verify before relying.

PDB2PQR prepares protein structures from PDB files for biomolecular simulations and continuum solvation calculations by automating structure setup, protonation, and parameterization tasks.

Yes, if you work with protein structures and need automated preparation for simulations or electrostatics calculations. The package is actively maintained, has no known vulnerabilities, installs with low friction, and carries a permissive license. It is purpose-built for a specific research workflow and unlikely to be useful outside structural biology or computational chemistry.

## Install

pip install pdb2pqr
uv add pdb2pqr
poetry add pdb2pqr

## Installing pdb2pqr

Before you install: Low friction installation with five runtime dependencies. Actively maintained as of 2026-04-26 with recent releases; supports Python 3.11–3.13.

License in practice: Permissive BSD-style license permits commercial and private use with attribution; redistribution in source or binary form allowed under standard BSD conditions.

Quickstart:

pip install pdb2pqr

from pdb2pqr import PDB2PQR

# Convert PDB structure to PQR format
pdb2pqr = PDB2PQR('input.pdb')
pdb2pqr.run()

Requires Python 3.11 or later; input PDB file must be provided and properly formatted.

Verify before relying:

- Whether the package includes built-in force field data or requires external parameterization files.
- Performance characteristics and typical runtime for large protein structures.
- Specific output format details and compatibility with downstream simulation software.

## Package facts

- License: Copyright (c) 2002-2024, Jens Erik Nielsen; Nathan A. Baker; Battelle Memorial Institute, Developed at the Pacific Northwest National Laboratory, operated by Battelle Memorial Institute, Pacific… (full text in the JSON record) (permissive)
- Python support: supports_current
- Install friction: low
- Maintenance: active
- Downloads: 430.2K/month (top 15,000 on PyPI)
- Known vulnerabilities: none known

## Tags

PDB structure preparation, protein protonation assignment, biomolecular simulation setup, continuum solvation calculations, PDB to PQR conversion, molecular structure parameterization, protein structure preprocessing, structural-biology, computational-chemistry, molecular-dynamics

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