ELECTROSTATICS ZONE

Electrostatics plays a very important role in Biochemistry. A few examples are: the estimation of the solvation free energy of a bio-molecular system, protein-ligand, protein-protein and protein-DNA interaction, pKa, protein structure. Implicit solvent modeling is a possible strategy for describing these phenomena. This approach can be justified in the context of classical continuum electrostatics and by a mean field approximation of the effects of the ionic solution consistent with the rules of statistical mechanics. Despite a certain degree of approximation, implicit methods are still of wide interest because of their algorithmic efficiency, due to the reduced number of degrees of freedom, and a relatively good compromise between model accuracy and efficiency. Among them, the Poisson-Boltzmann equation (PBE) approach is able to best capture the effects of the complex shapes arising at the nanoscale... We are part of the development team of DelPhi, a well known, Poisson-Boltzmann..