The Intrinsic Radius as a Key Parameter in the Generalized Born Model to Adjust Protein-Protein Electrostatic Interaction.

ABSTRACT: The generalized Born (GB) model is an extension of the continuum dielectric theory of Born solvation energy and is a powerful method for accelerating the molecular dynamic (MD) simulations of charged biological molecules in water. While the effective dielectric constant of water that varies as a function of the separation distance between solute molecules is incorporated into the GB model, adjustment of the parameters is indispensable for accurate calculation of the Coulomb (electrostatic) energy. One of the key parameters is the lower limit of the spatial integral of the energy density of the electric field around a charged atom, known as the intrinsic radius ρ. Although ad hoc adjustment of ρ has been conducted to improve the Coulombic (ionic) bond stability, the physical mechanism by wh

SUBMITTER: Parkin D 

PROVIDER: S-EPMC10003186 | biostudies-literature | 2023 Feb

REPOSITORIES: biostudies-literature