{"categories":[{"label":"Bio-Informatics","url":"https://skillfed.io/packages/category/scientific-engineering-bio-informatics"},{"label":"Chemistry","url":"https://skillfed.io/packages/category/scientific-engineering-chemistry"}],"enrichment":{"capability":"PDB2PQR prepares protein structures from PDB files for biomolecular simulations and continuum solvation calculations by automating structure setup, protonation, and parameterization tasks.","skillfed_tags":["structural-biology","computational-chemistry","molecular-dynamics"],"use_cases":["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."],"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\u2014tasks 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.\n\nThe 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.","worth_installing":"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."},"id":"pdb2pqr","links":{"html":"https://skillfed.io/packages/pdb2pqr","md":"https://skillfed.io/packages/pdb2pqr.md","pypi":"https://pypi.org/project/pdb2pqr/"},"maintenance":{"status":"active"},"meta":{"latest_release":"2024-12-28","license_spdx":null,"license_treatment":"permissive","name":"pdb2pqr","python_support":"supports_current","summary":"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."},"popularity":{"monthly_downloads":430186,"position":6730,"tier":"top_15000"},"security":{"n_vulnerabilities":0},"version":"3.7.1"}