  We present an extension of the Poisson-Boltzmann model in which the solute of
interest is immersed in an assembly of self-orienting Langevin water dipoles,
anions, cations, and hydrophobic molecules, all of variable densities.
Interactions between charges are controlled by electrostatics, while
hydrophobic interactions are modeled with a Yukawa potential. We impose steric
constraints by assuming that the system is represented on a cubic lattice. We
also assume incompressibility, i.e. all sites of the lattice are occupied. This
model, which we refer to as the Hydrophobic Dipolar Poisson Boltzmann Langevin
(HDPBL) model, leads to a system of two equations whose solutions give the
water dipole, salt, and hydrophobic molecule densities, all of them in the
presence of the others in a self-consistent way. We use those to study the
organization of the ions, co-solvent and solvent molecules around proteins. In
particular, peaks of densities are expected to reveal, simultaneously, the
presence of compatible binding sites of different kinds on a protein. We have
tested and validated the ability of HDPBL to detect pockets in proteins that
bind to hydrophobic ligands, polar ligands and charged small probes as well as
to characterize the environment of membrane proteins.
