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Biomolecular electrostatics software

What is here?

This website serves the following software packages for biomolecular modeling, solvation, and electrostatics.
  • APBS (Adaptive Poisson-Boltzmann Solver): software for evaluating the electrostatic properties of nanoscale biomolecular systems
  • PDB2PQR: an automated pipeline for the setup, execution, and analysis of Poisson-Boltzmann electrostatics calculations

What does it do?

We offer tutorials and background material for users interested in learning more about applying this software to their biomolecular modeling problem.  The following Wordle image summarizes the titles and abstracts from over 1700 papers that have cited APBS and PDB2PQR.

Start using APBS and PDB2PQR

You can start using these tools right away via the NBCR-hosted PDB2PQR web server, although we'd appreciate it if you register first to help us continue to support these software packages.

What is new?

  • PDB2PQR 1.8 released We are pleased to announce the release of PBD2PQR 1.8.  This version includes support for the new PROPKA 3.0 pKa software, several improvements to the command line extensions functionality, as well as improvements to the PDB2PQR web server.  A full list of changes is available in the release history page.As usual, PDB2PQR can be run through the web or downloaded for use on your computer.  Access to both the web server and the downloadable software is available at http://www.poissonboltzmann.org/pdb2pqr/d.Thank you for your continuing support of PDB2PQR.Sincerely,The PDB2PQR Development Team
    Posted Jan 26, 2012, 5:06 AM by Nathan Baker
  • New APBS 1.3 Windows Installer We have released a new version of the APBS Windows Installer with the following features:Ability to customize install path with correct behaviorInteractive command line interface when double-clicking APBS programThe new installer can be obtained through our downloads page.  Please let us know if you have any questions or concerns about this new installer.Thank you for your support of APBS.
    Posted Jan 4, 2012, 8:24 AM by Nathan Baker
  • An update on mailing lists Dear APBS users -- My apologies for the repeated posts on this subject but I wanted to update you on our troubled transition of the mailing lists to Google Groups. Unfortunately, it appears that many users have restricted access to Google Groups because of firewalls set by their countries and/or organizations.  Therefore, we will continue to host and archive the lists at two sites:  APBS-USERS can be accessed at https://lists.sourceforge.net/lists/listinfo/apbs-users or https://groups.google.com/forum/#!forum/apbs-usersAPBS-ANNOUNCEMENTS can be accessed at https://lists.sourceforge.net/lists/listinfo/apbs-announce or https://groups.google.com/forum/#!forum/apbs-announcements Messages posted to one list will be cross-posted to ...
    Posted Sep 21, 2011, 7:55 AM by Nathan Baker
  • PDB2PQR 1.7.1 released Dear PDB2PQR users -- We are pleased to announce the release of PDB2PQR 1.7.1.  This release contains several new features and bug fixes which are described in detail at http://goo.gl/w0BxD. Among these changes are several important features which should be of broad interest to the community.  The primary URL for APBS Opal support has changed to leverage services provided by the National Biomedical Computation Resource (http://nbcr.net/).  This provides additional computational resources to users who are interested in running calculations on remote resources. Added more JMol controls for visualization. Improved error reporting. Fixed many bugs in both the command line and web version. Improved behavior of –userff and –usernames command line switches for user created ...
    Posted Aug 6, 2011, 7:26 PM by Nathan Baker
  • APBS 1.3 released Dear APBS users -- We are pleased to announce the release of APBS 1.3.  This release contains several new features and bug fixes which are described in detail at http://goo.gl/l0Pt.  Among these changes are several important features which should be of broad interest to the community. The primary URL for APBS Opal support has changed to leverage services provided by the National Biomedical Computation Resource (http://nbcr.net/).  This provides additional computational resources to users who are interested in running calculations on remote resources, as described at http://goo.gl/CHZy.APBS now supports the ability to write out atom-specific potentials using the "write atompot" keyword in the APBS input file.  This has been an often ...
    Posted Oct 27, 2010, 7:56 AM by Nathan Baker
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