Remember, DelPhi webserver uses DelPhiPKa to add protons according to user specified pH. Hence, Delphi jobs may take twenty minutes to complete. Please be patient.
If you want the calculations to be fast, provide a PQR file instead.
Delphi Web Server
An online Poisson-Boltzmann solver for calculating electrostatic energies and potential in
Computational Biophysics & Bioinformatics - Dr. Emil Alexov Group
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
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
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
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
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.