Method and apparatus for estimating solvation energies of membrane bound molecules

A system for calculating a polar component of a solvation energy of a molecule, the molecule being partially embedded in a membrane and partially embedded in a solution, the system comprising:

• an analytical function determination module configured to determine, for each atom of the molecule that contributes to the polar component of the solvation energy of the molecule, a composite self-energy term of contribution to a polar component of a solvation energy of the atom made by the solution, the membrane, and other atoms of the molecule located at least partially inside the membrane, using an analytical function of atomic position relative to the midplane of said membrane in a region of the membrane where the molecule is embedded in the membrane including an empirical parameter;
• an atom polar component determination module configured to determine, for each atom of the molecule that contributes to the polar component of the solvation energy of the molecule, the polar component of the solvation energy of the atom, based on the composite self-energy term of the atom and a screening-effect term of the atom, the screening-effect term of the atom being a contribution to the polar component of the solvation energy of the atom made by other atoms of the molecule located at least partially outside the membrane;
• and
• a molecule polar solvation energy determination module configured to determine the polar component of the solvation energy of the molecule, based on the determined polar components of the solvation energies of all atoms of the molecule that contribute to the polar component of the solvation energy of the molecule;
• and an output for communicating results of the polar solvation energy determination module.

A method of estimating a polar component of a solvation energy of a molecule, the molecule being embedded in a first dielectric medium and a second dielectric medium having a different dielectric constant than the first dielectric medium, the first dielectric medium forming a substantially regular geometric shape, the method comprising:

• for each atom of the molecule, using an analytical function of atomic position relative to a location in the first dielectric medium to estimate a first term of contribution to a polar component of a solvation energy of the atom made by the first dielectric medium and other atoms of the molecule that are located in the first dielectric medium;
• for each atom of the molecule, determining a second term of contribution to the polar component of the solvation energy of the atom made by others atoms of the molecule that are located at least partially outside the first dielectric medium;
• for each atom of the molecule, combining the first term and the second term to determine the polar component of the solvation energy of the atom;
• and
• using the determined polar components of solvation energies of all atoms of the molecule to determine the polar component of the solvation energy of the molecule;
• and displaying one or more results of said polar solvation energy determination.

A method of estimating a polar component of a solvation energy of a molecule, the molecule being embedded in a first dielectric medium and a second dielectric medium having a different dielectric constant than the first dielectric medium, the first dielectric medium forming a substantially regular geometric shape, the method comprising:

• for each atom of the molecule, using an analytical function of atomic position relative to a location in the first dielectric medium to estimate a first term of contribution to a polar component of a solvation energy of the atom made by the first dielectric medium and other atoms of the molecule that are located in the first dielectric medium;
• for each atom of the molecule, determining a second term of contribution to the polar component of the solvation energy of the atom made by other atoms of the molecule that are located at least partially outside the first dielectric medium;
• for each atom of the molecule, using the first term and the second term to determine an effective Born radius of the atom;
• and
• using the determined effective Born radii of all atoms of the molecule to determine the polar component of the solvation energy of the molecule;
• and displaying one or more results of said polar solvation energy determination.