- DelPhi (software)
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DelPhi Operating system Linux, Mac OS X, Microsoft Windows Website Official DelPhi website 
Example of potential distribution in a system made of short peptide attached on dielectric plate and probed with a tip of atomic force microscope.
DelPhi is a scientific application which calculates electrostatic potential and energies in systems of biomolecules and geometrical objects. 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. Analytical solutions of the corresponding Poisson-Boltzmann equation (PBE) are not available for such cases and the distribution of the potential can be found only numerically. DelPhi, developed in Dr. Barry Honig lab in 1986, was the first PBE solver used by many researchers. The widespread popularity of DelPhi is due to its speed, accuracy (calculation of the electrostatic free energy is only slightly dependent on the resolution of the grid) and the ability to handle extremely high grid dimensions. Additional features such as assigning different dielectric constants to different regions of space, modeling geometric objects and charge distributions, and treating systems containing mixed salt solutions also attracted many researchers. 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.[1]PDB files are typically used as input for DelPhi calculations. Other required inputs are an atomic radii file and a charge file. Binary Potential files as output from DelPhi can be viewed in most molecular viewers, and can either be mapped onto surfaces or visualized at a fixed cutoff.[2]
DelPhi is commonly used in protein science to visualize variations in electrostatics along a protein or other macromolecular surface.[3]
References
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