DelPhi

It incorporates the effects of ionic strength mediated screening by evaluating the Poisson-Boltzmann equation at a finite number of points within a three-dimensional grid box.

[1] One of the main problems in modeling the electrostatic potential of biological macromolecules is that they exist in water at a given ionic strength and that they have an irregular shape.

In addition to the typical potential map, DelPhi can generate and output the calculated distribution of either the dielectric constant or ion concentration, providing the biomedical community with extra tools for their research.

[6] Binary Potential files as output from DelPhi can be viewed in most molecular viewers such as UCSF Chimera, Jmol, and VMD, and can either be mapped onto surfaces or visualized at a fixed cutoff.

[8] DELPHI has also been utilized to build a server that predicts pKa's of biological macromolecules such as proteins, RNAs and DNAs which can be accessed via web.