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

It would often be useful in computer simulations to use an implicit description of solvation
effects, instead of explicitly representing the individual solvent molecules. Continuum …

The binding free energy calculation of protein–ligand complexes is necessary for research
into virus–host interactions and the relevant applications in drug discovery. However, many …

The accurate prediction of protein–protein complex geometries is of major importance to
ultimately model the complete interactome of interacting proteins in a cell. A major …

The electrostatic properties of proteins arise from the number and distribution of polar and
charged residues. Electrostatic interactions in proteins play a critical role in numerous …

Developing a ligand with high affinity for a specific protein target is essential for drug design,
and water molecules are well known to play a key role in protein–drug recognition …

Calculation of protein–ligand binding affinity is a cornerstone of drug discovery. Classic
implicit solvent models, which have been widely used to accomplish this task, lack accuracy …

The electrostatic properties of proteins arise from the number and distribution of polar and
charged residues. Due to their long-ranged nature, electrostatic interactions in proteins play …

The current practical “workhorses” of the atomistic implicit solvation─ the Poisson–
Boltzmann (PB) and generalized Born (GB) models─ face fundamental accuracy limitations …

The interaction between eugenol and β-cyclodextrin in the presence of water is studied by
molecular mechanics and dynamics simulations. A force field model is used in molecular …