A generalized Born/surface area (GB/SA) water model (Qiu, D.; Shenkin, PS; Hollinger, FP;
Still, WCJ Phys. Chem. A 1997, 101, 3005− 3014) in combination with the GROMOS96 force …

Solvation is an important factor in the structure stabilization of proteins. The free energy of
solvation has been commonly approximated by summing the products of the atomic …

A computationally tractable strategy has been developed to refine protein-protein interfaces
that models the effects of side-chain conformational change, solvation and limited rigid-body …

Simplified models and empirical potentials are being increasingly used for the analysis of
proteins, frequently augmenting or replacing molecular mechanics approaches. Recent …

Implicit solvent models, in which the polar and nonpolar solvation free-energies of solute
molecules are treated separately, have been widely adopted for molecular dynamics …

The proximal distribution of water around proteins is a convenient method of quantifying
solvation. We consider the effect of charged and sulfur-containing amino acid side-chain …

An implicit solvent model (ISM) for use in molecular mechanics, Monte Carlo, and molecular
dynamics simulations on proteins and nucleic acids is proposed that is based on describing …

Accurate description of the solvent environment is critical in computer simulations of protein
structure and dynamics. An implicit treatment of solvent aims to capture the mean influence …

An analytical solvation model is proposed as a function of an order parameter, which
represents the local arrangement of water molecules in the first solvation shell of peptide …

Implicit solvent models for biomolecular simulations have been developed to use in place of
more expensive explicit models; however, these models make many assumptions and …