PDB2PQR
PDB2PQR converts PDB files to PQR format, adding missing atoms and assigning charges for electrostatics calculations.
Overview
PDB2PQR is an online tool designed to prepare structures from the Protein Data Bank (PDB) for electrostatics calculations. It provides a streamlined process to convert PDB files into PQR files, which are used as input for various computational biology and chemistry applications. Can also be used to fix common issue with PDB files.
Run PDB2PQR on Neurosnap
The PDB2PQR online webserver allows anybody with a Neurosnap account to run and access PDB2PQR, no downloads required. Information submitted through this webserver is kept confidential and never sold to third parties as detailed by our strong Terms of Use and Privacy Policy.
Features
- Converts PDB files to PQR format.
- Automatically adds missing heavy atoms and hydrogens.
- Optimizes the hydrogen bonding network.
- Assigns atomic charges and radii using multiple force fields (e.g., AMBER, CHARMM, PARSE, PEOEPB).
- Allows specification of force field.
- Predicts protonation states of titratable groups based on pKa calculations.
- Enables setting of pH for protonation state predictions.
- Provides options for optimizing hydrogen bonds.
- Produces PQR files with atomic coordinates, partial charges, and radii.
- Compatible with other computational tools for electrostatics calculations and molecular simulations.
- Can be integrated into custom pipelines and automation scripts.
- Handles a wide range of PDB structures, including those with non-standard residues and ligands.
Statistics
Neurosnap periodically calculates runtime statistics based on job execution data. These estimates provide a general guideline for how long your job may take, but actual runtimes can vary significantly depending on factors like input size or settings used.
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API Request
Access PDB2PQR using the Neurosnap API by sending a request using any programming language with HTTP support. To safely generate an API key, visit the API tab of your overview page.
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Citations
Please cite the original work when using PDB2PQR in publications or research outputs.
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PDB2PQR: expanding and upgrading automated preparation of biomolecular structures for molecular simulations. Dolinsky TJ, Czodrowski P, Li H, Nielsen JE, Jensen JH, Klebe G, Baker NA. Nucleic Acids Res. 2007 Jul;35(Web Server issue):W522-5. |
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PDB2PQR: an automated pipeline for the setup of Poisson-Boltzmann electrostatics calculations. Dolinsky TJ, Nielsen JE, McCammon JA, Baker NA. Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W665-7. |
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Neurosnap Inc. (2022). Neurosnap: An online platform for computational biology and chemistry. Available at: https://neurosnap.ai/ |