The Molecular Mechanics Poisson-Boltzmann Surface Area (MMPBSA) approach has been
widely applied as an efficient and reliable free energy simulation method to model molecular …

Free-energy calculations in the framework of classical molecular dynamics simulations are
nowadays used in a wide range of research areas including solvation thermodynamics …

The ability of atomic interaction parameters generated using the Automated Topology
Builder and Repository version 3.0 (ATB3. 0) to predict experimental hydration free …

This work provides a curated database of experimental and calculated hydration free
energies for small neutral molecules in water, along with molecular structures, input files …

The accurate prediction of protein− ligand binding free energies is a primary objective in
computer-aided drug design. The solvation free energy of a small molecule provides a …

Quantitative prediction of physical properties of liquids is important for many applications.
Computational methods based on either explicit or implicit solvent models can be used to …

Modern simulation and modeling approaches to investigation of biomolecular structure and
function rely heavily on a variety of methods—water models—to approximate the influence …

An increasing number of studies have reported computations of the standard (absolute)
binding free energy of small ligands to proteins using molecular dynamics (MD) simulations …

Molecular Mechanics Poisson–Boltzmann Surface Area (MMPBSA) methods have become
widely adopted in estimating protein–ligand binding affinities due to their efficiency and high …

Partition coefficients describe how a solute is distributed between two immiscible solvents.
They are used in drug design as a measure of a solute's hydrophobicity and a proxy for its …