Molecular docking is an established in silico structure-based method widely used in drug
discovery. Docking enables the identification of novel compounds of therapeutic interest …

This review describes the theory and implementation of implicit solvation models based on
continuum electrostatics. Within quantum chemistry this formalism is sometimes …

Molecular mechanics/Poisson–Boltzmann (Generalized-Born) surface area is one of the
most popular methods to estimate binding free energies. This method has been proven to …

ABSTRACT The General AMBER Force Field (GAFF) has been broadly used by researchers
all over the world to perform in silico simulations and modelings on diverse scientific topics …

Deep learning is an important branch of artificial intelligence that has been successfully
applied into medicine and two-dimensional ligand design. The three-dimensional (3D) …

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 …

Background and aim A novel coronavirus, called the severe acute respiratory syndrome
coronavirus 2 (SARS-CoV-2) has been found to cause COVID-19 in humans and some …

Protein–protein interactions form central elements of almost all cellular processes.
Knowledge of the structure of protein–protein complexes but also of the binding affinity is of …

Riboswitches can regulate gene expression by direct and specific interactions with ligands
and have recently attracted interest as potential drug targets for antibacterial. In this work …

The global pandemic crisis, coronavirus disease 2019 (COVID-19), caused by the severe
acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has claimed the lives of millions of …