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 …

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

AmberTools is a free and open-source collection of programs used to set up, run, and
analyze molecular simulations. The newer features contained within AmberTools23 are …

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 …

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 accuracy of computational models of water is key to atomistic simulations of biomolecules.
We propose a computationally efficient way to improve the accuracy of the prediction of …

The ability to estimate protein-protein binding free energy in a computationally efficient via a
physics-based approach is beneficial to research focused on the mechanism of viruses …

The ability to estimate protein-protein binding free energy in a computationally efficient via a
physics-based approach is beneficial to research focused on the mechanism of viruses …

Adaptive steered molecular dynamics (ASMD) is a computational biophysics method in which
an external force is applied to a selected set of atoms or a specific reaction coordinate to …

The use of fast in silico prediction methods for protein-ligand binding free energies holds
significant promise for the initial phases of drug development. Numerous traditional physics-…