Use PDB2PQR
Official Neurosnap webserver for accessing PDB2PQR online.
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.
Neurosnap Overview
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.
| Statistic | Value |
|---|---|
| Credit Usage Rate | loading... |
| Estimated Total Cost | loading... |
| Runtime Mean | loading... |
| Runtime Median | loading... |
| Runtime Standard Deviation | loading... |
| Runtime 90th Percentile | loading... |
| Runtime Longest | loading... |
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.
Similar Tools
Explore tools with similar features, categories, and use cases.
Job Note
Provide a name or description for your job to help you organize and track its results. This input is solely for organizational purposes and does not impact the outcome of the job.
Inputs & Configuration
Ready to submit your job?
Review your configuration, then confirm the estimated credit cost before you run the job.
Note that credit estimates are not guaranteed and runtime can vary depending on inputs and settings.
Estimated Credits: calculating...
To submit a job please login or register an account.