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.
Decision gist · record as of 2026-08-14
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.AI-flagged interpretation of the facts on this page — verify before relying
Before you install
- Requires Python 3.11 or later; input PDB file must be provided and properly formatted.
- Low friction installation with five runtime dependencies.
- Actively maintained as of 2026-04-26 with recent releases; supports Python 3.11–3.13.
License · maintenance · safety
permissive license (permissive) — Permissive BSD-style license permits commercial and private use with attribution; redistribution in source or binary form allowed under standard BSD conditions.
last release 2024-12-28 (594 days) · last repo commit 2026-04-26 · 174 stars
0 known vulnerabilities (OSV.dev, 2026-08-14) · 430,186 downloads/mo, #6,730 on PyPI
Alternatives
Verify before relying
pip install pdb2pqr
from pdb2pqr import PDB2PQR
# Convert PDB structure to PQR format
pdb2pqr = PDB2PQR('input.pdb')
pdb2pqr.run()- 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.
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 on this page. Verify before relying on it.
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
pdb2pqr on PyPI
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.
Requires Python 3.11 or later; input PDB file must be provided and properly formatted.
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()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 | permissive license permissive |
| Python support | Supports the current Python release <4,>=3.11 |
| Install friction | Low. Pure-Python wheel |
| Runtime dependencies | 5 packagesdocutilsmmcif-pdbxnumpypropkarequests |
| Maintenance | Actively maintained 594 days since the last release |
| Last repo commit | |
| First released | |
| Downloads | 430,186 / month, #6,730 on PyPI 30-day window, as of 2026-08-14 |
| Known vulnerabilities | None known OSV.dev, checked 2026-08-14 |
| Classifiers | Development Status :: 4 - BetaEnvironment :: ConsoleIntended Audience :: Science/ResearchLicense :: OSI Approved :: BSD LicenseNatural Language :: EnglishOperating System :: MacOSOperating System :: Microsoft :: WindowsOperating System :: POSIXProgramming Language :: PythonProgramming Language :: Python :: 3.11Programming Language :: Python :: 3.12Programming Language :: Python :: 3.13Programming Language :: Python :: Implementation :: CPythonTopic :: Scientific/Engineering :: Bio-InformaticsTopic :: Scientific/Engineering :: Chemistry |
Evidence: pdb2pqr-3.7.1-py3-none-any.whl
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See also mmcif-pdbx · propka · pydssp · pinder · prolif · pdbeccdutils · mdtraj · ase · biotraj · fastpdb