Delphi Web Server

An online Poisson-Boltzmann solver for calculating electrostatic energies and potential in biological macromolecules

Computational Biophysics & Bioinformatics - Dr. Emil Alexov Group

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DelPhi is a protein electrostatics program, originally developed in Dr. Barry Honig's lab and currently being maintained by Delphi Development team. It utilizes a finite difference method to solve the Poisson-Boltzmann equation for biomolecules and objects within a given system. Its benefits lie in the ability to solve linear or non-linear PB equations while being fast, versatile, and accurate. This webserver provides with an easy, straight-forward, and step-by-step process for using DelPhi for your own interests. Standalone Delphi package is available free of charge for download here.

A quick overview of how everything works:

  • A biomolecule coordinate file is needed (ie, PDB file format). This PDB file could sequentially be fixed for missing atoms/residues and protonated or the user can upload an already fixed and protonated file.
  • DelPhi uses charge and size files to gather information on the necessary atoms for your biomolecule. We provide these files as a default option, with them being produced for charmm, amber, or olpsaa compatibility. However, you are free to upload your own charge or size file, if need be.
  • A DelPhi paramter file is also needed for a successful submission. We provide a default parameter file . However, again, you are free to upload your own parameter file.
  • As for the results, you are given options for various energies to be calculated along with various visual display maps. For results to be automatically given, the user must provide name and email address.

DelPhi is running on Clemson University's Palmetto Supercomputer cluster. We would like to thank the Palmetto team for hosting this service. We also would like to acknowledge NIH-Grant# 1R01GM093937for supporting this work.

Finally, If these results appear in published papers, we ask humbly to include a reference to our service as defined here.

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