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 …

Important properties of globular proteins, such as the stability of its folded state, depend
sensitively on interactions with solvent molecules. Existing methods for estimating these …

Applying a very simple approximation to the solvation potential theory of Chandler and co-
workers enables the derivation of a surface accessible area solvation potential model that …

We have performed molecular dynamics simulations of protein surface loops solvated by
explicit water, where a prime focus of the study is the small numbers (eg,∼ 100) of explicit …

The burial of hydrophobic amino acids in the protein core is a driving force in protein folding.
The extent to which an amino acid interacts with the solvent and the protein core is naturally …

Increasingly complex schemes for representing solvent effects in an implicit fashion are
being used in computational analyses of biological macromolecules. These schemes speed …

Background: The tractability of many algorithms for determining the energy state of a system
depends on the pairwise nature of an energy expression. Some energy terms, such as the …

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 …

Implicit solvent hydration free energy models are an important component of most modern
computational methods aimed at protein structure prediction, binding affinity prediction, and …

Consistent approaches for calculations of solvation free energies should provide results
which are independent of the size of the simulation region. Simulations that use periodic …