Colloquium - DelPhi Poisson-Boltzmann solver: Improvements and applications.

Electrostatics plays major role in molecular biology because practically all atoms carry partial charge and are situated at Angstroms distances. In addition, the electrostatic force is a long-range force, in contrast with other forces present in biological systems, and thus provides guiding for many reactions involving charged objects. However, modeling electrostatic potential and computing electrostatic energies is not trivial task because biological macromolecules function in water phase. To overcome the complexity of the water phase one applies continuum electrostatics to deliver the potential distribution, considering that the water and macromolecules are two distinctive dielectric media. Here we report development of a Gaussian model to deliver a smooth dielectric function which is implemented in DelPhi. The performance of the Gaussian DelPhi is benchmarked against solvation energies of small molecules obtained with explicit water simulations and very good agreement is found. The Gaussian DelPhi is also shown to perform much better than standard calculations in delivering the potential distribution in the reaction center protein. Furthermore we report a parallelized DelPhi, which speed is more than 100 times faster than the sequential DelPhi while delivering the same potential and energies.  Several applications are outlined as well showing the importance of electrostatics in modeling biological systems.