Molecular mechanics Poisson–Boltzmann surface area (MM/PBSA) and molecular
mechanics generalized Born surface area (MM/GBSA) are arguably very popular methods …

Introduction: The molecular mechanics energies combined with the Poisson–Boltzmann or
generalized Born and surface area continuum solvation (MM/PBSA and MM/GBSA) methods …

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

A central quantity of interest in molecular biology and medicine is the free energy of binding
of a molecule to a target biomacromolecule. Until recently, the accurate prediction of binding …

Computational studies play an increasingly important role in chemistry and biophysics,
mainly thanks to improvements in hardware and algorithms. In drug discovery and …

We have performed a systematic study of the entropy term in the MM/GBSA (molecular
mechanics combined with generalized Born and surface-area solvation) approach to …

The accurate prediction of the binding affinities of ligands to proteins is a major goal in drug
discovery and personalized medicine. The time taken to make such predictions is of similar …

Binding free energy calculations that make use of alchemical pathways are becoming
increasingly feasible thanks to advances in hardware and algorithms. Although relative …

Molecular dynamics simulation is now a widespread approach for understanding complex
systems on the atomistic scale. It finds applications from physics and chemistry to …

The use of molecular simulation to estimate the strength of macromolecular binding free
energies is becoming increasingly widespread, with goals ranging from lead optimization …