CMIRS (composite method for implicit representation of solvent) is a relatively new implicit solvation model that adds terms representing solute-solvent dispersion, Pauli repulsion, and hydrogen bonding to a continuum treatment of electrostatics. A small error in the original implementation of the dispersion term, but one that can modify dispersion energies by up to 8 kcal/mol in some cases, ne...

Implicit solvent models are increasingly popular for estimating aqueous solvation (hydration) free energies in molecular simulations and other applications. In many cases, parameters for these models are derived to reproduce experimental values for small molecule hydration free energies. Often, these hydration free energies are computed for a single solute conformation, neglecting solute confor...

Central in the variational implicit-solvent model (VISM) [Dzubiella, Swanson, and McCammon Phys. Rev. Lett.2006, 96, 087802 and J. Chem. Phys.2006, 124, 084905] of molecular solvation is a mean-field free-energy functional of all possible solute-solvent interfaces or dielectric boundaries. Such a functional can be minimized numerically by a level-set method to determine stable equilibrium confo...

BACKGROUND The number of high-resolution structures of pharmacologically relevant membrane proteins has been strongly increasing. This makes computing relative affinities of chemically similar compounds binding to a membrane protein possible in order to guide decision making in drug design. However, the preparation step of such calculations is time-consuming and complex. METHODS We extended t...

Geometric singularities, such as cusps and self-intersecting surfaces, are major obstacles to the accuracy, convergence, and stability of the numerical solution of the Poisson-Boltzmann (PB) equation. In earlier work, an interface technique based PB solver was developed using the matched interface and boundary (MIB) method, which explicitly enforces the flux jump condition at the solvent-solute...

The binding affinity between a probe hydrophobic particle and model hydrophobic plates with different charge (or dipole) densities in water was investigated through molecular dynamics simulation free-energy perturbation calculations. We observed a reduced binding affinity when the plates are charged, in agreement with previous findings. With increased charge density, the plates can change from ...

A new implicit solvent model for computing the electrostatics binding free energy in protein-ligand docking is proposed. The new method is based on an adaptation of the screening coulombic potentials proposed originally by Hassan et al. (J Phys Chem B 2000;104:6490-6498). In essence, it relies on two basic assumptions; (i) solvent screening can be accounted for by means of radially dependent si...