Contact surface area and chemical properties of atoms are used to concurrently predict
conformations of multiple amino acid side chains on a fixed protein backbone. The …

The anisotropy of shape and functionality of proteins complicates the prediction of protein–
protein interactions. We examine the distribution of electrostatic and nonelectrostatic …

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 …

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 …

When simulating protein adsorption behavior, decisions must first be made regarding how
the protein should be oriented on the surface. To address this problem, we have developed …

Solvation effects are critically important in the structural stabilization and functional
optimization of proteins. Here, we propose a new solvation free energy function for proteins …

A reliable theoreticaltreatment of chemical processes which occur in aqueous solution
requires accurate methods for calcu-lating solvation free energies. A number of theoretical …

A polarizable force field, and associated continuum solvation model, have been developed
for the explicit purpose of computing and studying the energetics and structural features of …

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 …

Implicit solvent models are important for many biomolecular simulations. The polarity of
aqueous solvent is essential and qualitatively captured by continuum electrostatics methods …