Generalized born model: Analysis, refinement, and applications to proteins

A Generalized Born (GB) model, describing the mean-field electrostatic energy of a molecular system in a continuous, polarizable solvent environment, is compared with Kirkwood and Poisson-Boltzmann (PB) standard approaches. GB energy data for amino acids, a dodecapeptide, and three protein molecules are validated against the corresponding PB numerical results. A new approximation for the Born radii, dependent on the geometry of the system, as well as on the ratio of the solute and solvent dielectric constants, is proposed. The refined GB approach also takes into account the ionic strength. The most important discrepancies between the GB and PB results for proteins are identified and interpreted. A more precise procedure for computing the GB energy is proposed.