Welcome to the SDPBS Web Server

SDPBS (Solution Decomposition Poisson-Boltzmann Solvers) is a library of solvers for the Poisson-Boltzmann equation (PBE). This library utilizes several computational methods, including finite element, finite difference, solution decomposition, domain decomposition, and multigrid techniques. A related platform, the SMPBS web server is available, which implements a size-modified Poisson-Boltzmann model. Together, these recourses form a robust toolkit for biochemists, biophysicists, bioengineers, and medical scientists for tackling a wide range of computational chemistry, computational biology, and molecular modeling problems.

Applications of the SDPBS Web Server

The SDPBS web server can be used to calculate the electrostatic solvation energy of a biomolecule, and the binding energy of a biomolecular complex.

To get started, click on one of the links below. Please ensure that Javascript is enabled in your browser to access the SDPBS web server's user-friendly interface.

Calculate the electrostatic solvation energy of a biomolecule

Using the SDPBS Web Server

Before submitting a job, prepare the PQR file(s) of a biomolecule by performing the following steps:

After preparing a PQR file, the user should:

  1. Upload the PQR file.
  2. Adjust basic and/or advanced parameters.
  3. Submit the job.
  4. Download result files, if desired.
  5. Visualize results, if desired.

User workflow diagram
Diagram of of SDPBS user workflow.

Credits

SDPBS was developed by Professor Dexuan Xie and his research group in the Department of Mathematical Sciences at the University of Wisconsin-Milwaukee. The SDPBS web server was conceived by Professor Xie, in collaboration with Professor Zeyun Yu, of the Department of Computer Science at the University of Wisconsin-Milwaukee. Initial web design and programming was implemented by (in alphabetical order) Yi Jiang, Jeremy Streich, and Yang Xie. The web server is currently hosted by the University of Wisconsin-Milwaukee L&S IT Office.

Update History

  • 08/01/23 - Updated home page, toolbar. - MD
  • 04/04/16 - Added JSmol visualization, AJAX submissions, more instructions; tweaked layout - YX
  • 12/16/15 - Added parameter tooltips, added spinner, tweaked layout - YX
  • 11/28/15 - Added "About" section, revised/edited text - YX
  • 11/13/15 - Initial release.