Welcome to the SDPBS Web Server (Updated 04/04/16)

Solution Decomposition Poisson-Boltzmann Solvers (SDPBS) is a library of Poisson-Boltzmann equation solvers that incorporates finite element, finite difference, solution decomposition, domain decomposition, and multigrid techniques.

This web server allows researchers to use SDPBS to calculate PBE solutions and visualize biomolecules remotely. As an application, it can be used to calculate the electrostatic solvation energy of a biomolecule in ionic solvent, as well as the binding energy of a biomolecule complex. Click the links below to get started:

How To

Before submitting a job, prepare a PQR file of a biomolecule. This can be done by first downloading a PDB file of the biomolecule from the RCSB Protein Data Bank, and then converting it to a PQR file by using PDB2PQR. After preparing the 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. The website is currently updated and maintained by Yang Xie.

Update history

  • 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.