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 …

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 …

We present a physically rigorous method to calculate solvent-dependent accessible surface
areas (ASAs) of amino acid residues in unfolded proteins. ASA values will be larger in a …

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 …

This paper reviews a recently developed method for calculating the total conformational free
energy of a solute macromolecule in water solvent. The method consists of a relatively short …

Electrostatics and solvation energies are important for defining protein stability, structural
specificity, and molecular recognition. Because these energies are difficult to compute …

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

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

The prediction of protein–protein interactions in solution is a major goal of theoretical
structural biology. Here, we implement a continuum description of the thermodynamic …

In aqueous solution, the ensemble of conformations sampled by peptides and unfolded
proteins is largely determined by their interaction with water. It has been a long‐standing …