Accuracy of protein–ligand binding free energy calculations utilizing implicit solvent models
is critically affected by parameters of the underlying dielectric boundary, specifically, the …

Accurate yet efficient computational models of solvent environment are central for most
calculations that rely on atomistic modeling, such as prediction of protein–ligand binding …

Ligand binding affinity prediction is one of the most important applications of computational
chemistry. However, accurately ranking compounds with respect to their estimated binding …

Physics-based force fields for ligand–protein docking usually determine electrostatic energy
with distance-dependent dielectric (DDD) functions, which do not fully account for the …

Fast and accurate calculation of solvation free energies is central to many applications, such
as rational drug design. In this study, we present a grid-based molecular surface …

One of the most important biological processes at the molecular level is the formation of
protein–ligand complexes. Therefore, determining their structure and underlying key …

Water molecules in the binding pocket of a protein and their role in ligand binding have
increasingly raised interest in recent years. Displacement of such water molecules by ligand …

Rigorous binding free energy methods in drug discovery are growing in popularity because
of a combination of methodological advances, improvements in computer hardware, and …

ABSTRACT A new implicit solvent model for computing the electrostatics binding free
energy in protein–ligand docking is proposed. The new method is based on an adaptation of …

An ultrafast and accurate scoring function for protein–protein docking is presented. It
includes (1) a molecular mechanics (MM) part based on a 12–6 Lennard-Jones potential;(2) …