Molecular dynamics (MD) simulations have become increasingly useful in the modern drug
development process. In this review, we give a broad overview of the current application …

Metadynamics is a popular enhanced sampling algorithm for computing the free energy
landscape of rare events by using molecular dynamics simulation. Ten years ago, Tiwary …

S-Adenosyl-l-methionine (SAM)-responsive riboswitches play a central role in the regulation
of bacterial gene expression at the level of transcription attenuation or translation inhibition …

A consensus virtual screening protocol has been applied to ca. 2000 approved drugs to
seek inhibitors of the main protease (Mpro) of SARS-CoV-2, the virus responsible for COVID …

Lipids play important modulatory and structural roles for membrane proteins. Molecular
dynamics simulations are frequently used to provide insights into the nature of these protein …

Caver Web 1.0 is a web server for comprehensive analysis of protein tunnels and channels,
and study of the ligands' transport through these transport pathways. Caver Web is the first …

Calculations of ligand binding free energies and kinetic rates are important for drug design.
However, such tasks have proven challenging in computational chemistry and biophysics …

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 …

In this review, we outline the growing role that molecular dynamics simulation is able to play
as a design tool in drug delivery. We cover both the pharmaceutical and computational …