Method and apparatus for estimating solvation energies of membrane bound molecules

摘要

The disclosure relates to a method of estimating the polar component of the solvation energy for a molecule embedded in different media. In one embodiment, the molecule is partially embedded in a membrane. For an atom of the molecule, the polar component of the atom's solvation energy is represented as a combination of at least a self-energy term and a screening-effect term. The self-energy term represents the contribution to the atom's polar component made by the membrane and the molecule's other atoms located inside the membrane. The screening-effect term represents the typically negative contribution to the atom's polar component made by the molecule's other atoms located outside the membrane. An analytical function is used to calculate the self-energy term. In a preferred embodiment, the analytical function is a function of the distance from the atom to the membrane, the van der Waals radius of the atom, and the thickness of the membrane. The effective Born radius of the atom is then determined based on its polar component. The effective Born radii of the atoms are then used to determine the polar component of the solvation energy for the molecule.