A refined implicit aqueous solvation model is proposed for the simulation of biomolecules
without the explicit inclusion of the solvent degrees of freedom. The mean force due to …

An empirical solvation model that allows for the elimination of solvent degrees of freedom in
molecular dynamics (MD) simulations of biomolecules is proposed. The potential of mean …

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 solvation term based on the solvent accessible surface area (SASA) is combined with the
CHARMM polar hydrogen force field for the efficient simulation of peptides and small …

The influence of solvent on the individual amino acids of a protein depends not simply on
their surface exposure but rather on the degree of their burial within the structure. This …

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 …

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 …

Modern implicit solvent models for macromolecular simulations in water–proton bath are
considered. The fundamental quantity that implicit models approximate is the solute …

Abstract Models of protein structure are frequently used to determine the physical
characteristics of a protein when the crystal structure is not available. We developed a …

The solvent environment of molecules plays a very important role in their structure and
function. In biological systems it is well known that water has profound effects in the …