Designing a reliable computational methodology to calculate protein: ligand standard
binding free energies is extremely challenging. The large change in configurational enthalpy …

Many mammals use scent marks to advertise territory ownership, but only recently have we
started to understand the complexity of these scent signals and the types of information that …

INTRODUCTION Climate extremes create a need to mitigate the effects of drought on
agriculture. The contributions of water to crop yield vary over a growing season but peak …

The hydrophobic effect—a rationalization of the insolubility of nonpolar molecules in water—
is centrally important to biomolecular recognition. Despite extensive research devoted to the …

Biomolecular recognition can be stubborn; changes in the structures of associating
molecules, or the environments in which they associate, often yield compensating changes …

It is well-established that dynamics are central to protein function; their importance is
implicitly acknowledged in the principles of the Monod, Wyman and Changeux model of …

Hydrophobic association is often recognized as being driven by favorable entropic
contributions. Here, using explicit solvent molecular dynamics simulations we investigate …

Proteins are dynamic entities, and they possess an inherent flexibility that allows them to
function through molecular interactions within the cell, among cells and even between …

Rational drug design is predicated on knowledge of the three-dimensional structure of the
protein− ligand complex and the thermodynamics of ligand binding. Despite the …

An efficient molecular simulation methodology has been developed to determine the
positioning of water molecules in the binding site of a protein or protein− ligand complex …